Nabble - Bio.net - Mol-evol

diatom dna

2009-10-28T03:48:18Z

Dear,

Can you send me the CTAB protocol for DNA extraction in diatoms,

Thanks in advance.

Drs. Ives Vanstechelman

--
==================================================================
Ives Vanstechelman

Tel:+32 (0)9 331 38 63 fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
ivste@... http://www.psb.vib-ugent.be
==================================================================

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Lectureship vacancy in evolutionary biology at York, UK

2009-09-24T05:38:30Z

We are currently advertising for a lecturer in evolutionary biology (a
permanent position) here in the Biology Department at York. If you know
of any potentially suitable candidates, please draw this opportunity to
their attention, or let me have their details and I will be happy to
contact them.

The closing date is 8 October, and details can be found at
https://www22.i-grasp.com/fe/tpl_YorkUni01.asp?newms=jj&id=28579

Peter Young

--
Prof J P W Young
Department of Biology 3
University of York
P O Box 373
York YO10 5YW, UK

jpy1@... tel: +44 1904 328630(direct), 328500(department)
fax: +44 1904 328505(department)
http://www.york.ac.uk/depts/biol/staff/jpwy/jpwy.htm

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

TIPDATE

2009-08-28T01:54:34Z

Dear Sir,

I would like to tray your tipdate on my EAV sequences.

Thank you, sara from Slovenia

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Introduction to Bioinformatics, October 2009

2009-08-18T02:38:41Z

The online course, Introduction to Bioinformatics, is designed to
provide professional development for biologists working in a wide range
of different areas. Students successfully completing the assessments
will receive a certificate from The University of Manchester.

Like all of our distance courses, it is delivered in a Virtual Learning
Environment that allows us to extend the classroom into the web. We use
a range of tools to support our online teaching activities.

Teaching and learning are focussed around tutor-supported exercises. In
this course, participants work together on the interpretation of their
results, before receiving feedback from the course tutor.

Week 1 Introduction to distance learning
Bioinformatics as a knowledge-based discipline

Weeks 2 and 3 Introduction to the sequence databases
Quality, redundancy and annotation
Sequence retrieval exercise and group discussion

Weeks 4 and 5 Nucleic acid sequence analysis

Weeks 6 and 7 Independent research and assessment

Weeks 8 and 9 Sequence alignment and database search

Weeks 10 and 11 Protein function prediction.

Weeks 12 and 13 Protein structure prediction
Practical exercise and group discussion

Weeks 14 to 16 Independent research for the second assessment

You will find information on all our courses, including fees and a link
to the online application form, here :
http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any
questions, or need advice on the module options, please contact
Heather.Vincent from manchester.ac.uk

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Conference, Comparative Genomics, University of St Andrews

2009-08-04T09:14:32Z

Dear bionet.molbio.evolution,

* * * * * * * * * * * * * * *

Comparative Genomics One-day International Conference
Date: 18th August 2009, 9:30 am
Location: Bute Building, University of St Andrews, UK

* * * * * * * * * * * * * * *

This is a one day event - A day of exciting talks on comparative
genomics from an array of international speakers.

Thousands of genome sequences are now available, and the amount of data
on genomes continues to increase. This presents enormous opportunities
to make discoveries of biological and medical interest, but also
requires new approaches.

Confirmed speakers:

o Prof MARK BLAXTER, University of Edinburgh. "Comparative Nematode
Genomics".
o Prof GEOFF BARTON, University of Dundee. "A tale of three small RNAs".
o Prof DANNIE DURAND, Carnegie Mellon University. "The Evolution of
Multidomain Families".
o Prof NEIL HALL, University of Liverpool. "Fast forward Genetics using
second generation sequencing".
o Dr MATTHEW HEGARTY, Aberystwyth University. "Genomic mergers: the
consequences of hybridisation and polyploidy in Senecio".
o Prof IAN KORF, University of California Davis Genome Center. "Intron
mediated enhancement".
o Prof ALAN ARCHIBALD FRSE, Roslin Institute. "Comparative farm animal
genomics - from synteny to synergy".
o Dr ZEMIN NING, Wellcome Trust Sanger Institute. "Cancer genome
assemblies and variation detection between normal and tumor human cells".
o Prof ZIHENG YANG FRS, University College London. "Population genomics
and human-chimpanzee speciation".
o Prof ANDY WATERS, University of Glasgow, "Translation of Translation:
Comparative genomics yields practical insights into sexual development
in malaria parasites".

More information can be found at http://www.sbforum.org/events.php?e_id=70

Registration details:

Early registration is encouraged. Registration fees are GBP 40; students
can register for a reduced fee of GBP 20.

** Please register on-line at: http://www.sbforum.org/eregister.php?e_id=70

The event is preceded by a conference dinner, at a subsidized price for
conference delegates. Please book in advance.
http://www.sbforum.org/events.php?e_id=76

The conference itself is followed by a networking buffet dinner,
included in the registration fee.

Poster submission:

Delegates are welcome to submit an abstract on any aspect of comparative
genomics. The poster abstract deadline has been extended to Thursday
13th August.

* * * * * * * * * * * * * * *

We look forward to seeing you on Tuesday 18th August.

Best regards,

Daniel

--
Daniel Barker
http://bio.st-andrews.ac.uk/staff/db60.htm
The University of St Andrews is a charity registered in Scotland :
No SC013532

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Palindrome and non-palindrome

2009-06-23T04:43:52Z

Dear Dr. Gegenheimer,
I hope this e-mail finds you well.

I sought that you gave some reasons to explain why palindromic recognition sequences.
I found that you answer is very reasonable and indeed, because the risk or having this flanks the bacteria avoid those sequences. However, what about non-palindromic restriction sites? Those are avoided too, but are those as important as palindromic sequences? The non-symmetric restriction sites will be target of a single-stranded cleavage or same as palindrome, the enzymes can cut both DNA strands?

I will really appreciate your input.

Ana Luisa

--
Ana Luisa Maldonado-Contreras
PhD Candidate
University of Puerto Rico
Rio Piedras Campus
Microbial Ecology Lab
Phone: 787 764 0000 ext. 4883

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Conference, Comparative Genomics, University of St Andrews

2009-05-14T04:38:31Z

Dear bionet.molbio.evolution,

I would like to draw your attention to these events in St Andrews this
August:

- One day conference, "Comparative Genomics"
- Summer school, "Bioinformatics and Comparative Genomics"
- Workshop, "The Role of Behaviour in Speciation"

Details are below.

*****************************************************************
Comparative Genomics one-day international conference

Date: 18th August 2009
Location: Bute Building, University of St Andrews, UK
*****************************************************************

The Scottish Bioinformatics Forum and the University of St Andrews are
pleased to announce a one-day international conference, "Comparative
Genomics", with nine invited speakers and an open poster session.

Confirmed speakers:

- Prof MARK BLAXTER, University of Edinburgh. "Comparative nematode
genomics".
- Prof GEOFF BARTON, University of Dundee. "A tale of three small RNAs".
- Prof DANNIE DURAND, Carnegie Mellon University. "The evolution of
multidomain families".
- Prof NEIL HALL, University of Liverpool. "Fast forward genetics using
second generation sequencing".
- Dr MATTHEW HEGARTY, Aberystwyth University. "Genomic mergers: the
consequences of hybridisation and polyploidy in Senecio".
- Prof IAN KORF, University of California Davis Genome Center. "Intron
mediated enhancement".
- Dr DAVID MARTIN, University of Dundee. "Predicting protein function".
- Dr ZEMIN NING, Wellcome Trust Sanger Institute. "Cancer genome
assemblies and variation detection between normal and tumor human cells".
- Prof ZIHENG YANG FRS, University College London. "Population genomics
and human-chimpanzee speciation".

For more information on the conference, including registration and
poster abstract submission, please see:

http://www.sbforum.org/events.php?e_id=70

*****************************************************************
Summer School - Bioinformatics and Comparative Genomics

Start Date: 15th August 2009, 9:00 am
End Date: 18th August 2009 (including one-day conference)
Location: University of St Andrews, UK
*****************************************************************

The Scottish Bioinformatics Forum and the University of St Andrews are
pleased to announce the first Summer School on Bioinformatics and
Comparative Genomics. The summer school will address practical
bioinformatics for sequence analysis and comparative genomics, for use
in biological and biomedical research.

The summer school will be held in St Andrews on 15th-17th August 2009.
Registration for the summer school also includes attendance at the
one-day conference on Comparative Genomics on 18 August (see above).

Confirmed tutors:

- Prof ZIHENG YANG FRS, University College London
- Dr ZEMIN NING, Wellcome Trust Sanger Institute
- Dr DAVID MARTIN, University of Dundee
- Prof IAN KORF, University of California Davis Genome Center
- Dr CHRIS JANSSEN, SBF and University of Glasgow
- Prof NEIL HALL and Dr ALISTAIR DARBY, University of Liverpool
- Dr DAVID FERRIER, University of St Andrews
- Prof DANNIE DURAND, Carnegie Mellon University
- Prof GEOFF BARTON and Dr JIM PROCTER, University of Dundee
- Dr DANIEL BARKER, University of St Andrews

For more information on the summer school and registration details,
please see:

http://www.genome-bioinformatics.org/index.html

*****************************************************************
Workshop - The Role of Behaviour in Speciation

Start Date: 19th August 2009
End Date: 22nd August 2009
Location: University of St Andrews, UK
*****************************************************************

This is a separate workshop at St Andrews, arranged by the EU Marie
Curie Initial Training Network "SPECIATION". Details of this workshop
are available from Prof Mike Ritchie:

http://biology.st-andrews.ac.uk/staff/mgr.htm

and will appear at:

http://speciation.group.shef.ac.uk

Looking forward to seeing you in St Andrews!

Kind Regards

Daniel Barker

--
Daniel Barker
http://bio.st-andrews.ac.uk/staff/db60.htm
The University of St Andrews is a charity registered in Scotland :
No SC013532

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

selection in expanding populations

2009-04-14T10:03:17Z

Hi,
I would like to compile some references concerning the detection of selection using molecular data in expanding populations. Especially I am interested in both theoretical and applied studies. Any suggestions for seminal papers would be greatly appreciated. I would also be interested in hearing your critical impressions on this pursuit.
Sarah
_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Course: St Andrews, Scotland, Bioinformatics and Comparative Genomics, 15-18 August 2009

2009-04-10T06:13:20Z

The University of St Andrews and the Scottish Bioinformatics
Forum will be hosting:

Summer School - Bioinformatics and Comparative Genomics
Start Date: 15th August 2009, 09:00 am
End Date: 18th August 2009
Location: The University of St Andrews, Scotland

http://www.genome-bioinformatics.org

Confirmed Speakers:
Prof Ziheng Yang FRS, University College London, UK
Prof Neil Hall, University of Liverpool, UK
Dr Zemin Ning, Wellcome Trust Sanger Institute, UK
Dr David Martin, University of Dundee, UK
Prof Geoff Barton, University of Dundee, UK
Dr Daniel Barker, University of St Andrews, UK
Prof Ian Korf, UC Davis Genome Center, USA
Prof Dannie Durand, Carnegie Mellon University, USA
Dr Chris Janssen, SBF and University of Glasgow, UK
Dr David Ferrier, University of St Andrews, UK

The summer school on bioinformatics and comparative genomics
will address practical bioinformatics for sequence analysis
and comparative genomics for use in biological and
biomedical research. Internationally renowned invited
speakers will discuss current challenges, applications, and
future outlook in the field. The school will consist of a
series of lectures, seminars and practical classes, allowing
participants both insight into theory and the opportunity to
learn practical skills in data analysis and interpretation.

Registration for the summer school includes attendance at a
one-day international conference on 18th August,
"Comparative Genomics". Four nights of accommodation
(14th-17th August) are optionally available on registration.

Full details and registration please see:

http://www.genome-bioinformatics.org

We look forward to seeing you in August.

Best regards,

Daniel

--
Daniel Barker
http://bio.st-andrews.ac.uk/staff/db60.htm
The University of St Andrews is a charity registered in Scotland :
No SC013532

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Last call: Bioinformatics and Comparative Genome Analysis EMBO course in Hong Kong

2009-04-07T10:35:12Z

Last Call for application to the :

Bioinformatics and Comparative Genome Analysis course
August 17 - August 29, 2009
HKU-Pasteur Research Centre - Hong Kong

Deadline for application: April 15, 2009.

Course program: http://www.pasteur.fr/~tekaia/BCGA2009/
BCGA2009_Prog.html

Duration: Full time from August 17 to August 29, 2009.

Location:
Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong
Kong SAR, China.

Accommodation and social: Acceptance to the course includes free
accommodation (double room based) breakfast, lunch and dinner.

More information about the course, how to apply and application form
can be found at the course web page: http://www.pasteur.fr/~tekaia/
BCGA2009.html

Organizers/Contact:
Roberto Bruzzone, HKU-Pasteur Research Centre - Hong Kong.
Si Lok, Genome Research Center The University of Hong Kong - Hong Kong.
Tin Wee Tan, National University of Singapore - Singapore.
Ueng-Cheng Yang, National Yang-Ming University, Taipei - Taiwan.
Fredj Tekaia, Institut Pasteur Paris - France.

With financial support from:
EMBO - Institut Pasteur Paris.

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

IICAI-09 Final Call for papers

2009-04-04T12:22:26Z

*Apologies if you received multiple copies of this email. Please forward to interested people*

IICAI-09 Final Call for papers

http://www.iiconference.org

The 4^th Indian International Conference on Artificial Intelligence (IICAI-09) will be held in Tumkur (near Bangalore), India during December 16-18 2009. This is one of the biggest AI events in the world and fuses on all areas of AI and its applications. The conference consists of paper presentations, special workshops, sessions, invited talks and local tours, etc. We invite draft paper submissions. The paper submission deadline is just few weeks from now. Please see the website: http://www.iiconference.org for more details of the conference.

Sincerely

Eugene

Publicity Committee

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Bioinformatics and Comparative Genome Analysis EMBO course in Hong Kong

2009-02-23T09:22:10Z

Call for application to the :

Bioinformatics and Comparative Genome Analysis course
August 17 - August 29, 2009
HKU-Pasteur Research Centre - Hong Kong

Course web page: http://www.pasteur.fr/~tekaia/BCGA2009.html
Course program: http://www.pasteur.fr/~tekaia/BCGA2009/
BCGA2009_Prog.html

Aim of the course:

The main objectives of the course are to familiarize young scientists
(Biologists/Computer Scientists/Mathematicians) with bioinformatics
and genome data analysis skills and to encourage multi-disciplinarity
by introducing:

1- advanced fundamental algorithms in bioinformatics,
2- their application in genome analyses,
3- and recent knowledge acquired from genomes studies and perspectives.

The course is aimed for motivated Ph.D, Post-doctoral students, as
well as young assistant professors and junior scientists in Public
Institutions particularly from Asia, Australia, Africa and South
America, with background in Mathematics, Statistics, Biology or
Computing, who are involved in Bioinformatics and Genomes studies.

Duration: Full time from August 17 to August 29, 2009.

Location:
Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong
Kong SAR, China.

Accommodation and social: Acceptance to the course includes free
accommodation (double room based) breakfast, lunch and dinner.

Application Deadline: April 15, 2009.

More information about the course, how to apply and application form
can be found at the following web page: http://www.pasteur.fr/~tekaia/
BCGA2009.html

Organizers/Contact:
Roberto Bruzzone, HKU-Pasteur Research Centre - Hong Kong.
Si Lok, Genome Research Center The University of Hong Kong - Hong Kong.
Tin Wee Tan, National University of Singapore - Singapore.
Ueng-Cheng Yang, National Yang-Ming University, Taipei - Taiwan.
Fredj Tekaia, Institut Pasteur Paris - France.

With financial support from:
EMBO - Institut Pasteur Paris.

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Paper submission deadline extended: MULTICONF-09

2009-02-03T08:23:36Z

Paper submission deadline extended: MULTICONF-09

The deadline for draft paper submission at the 2009 Multi Conference in Computer Science, Information Technology and Control systems and Computational Science and Computer Engineering (MULTICONF-09) (website: http://www.PromoteResearch.org) is extended due to numerous requests from the authors. The conference will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The event consists of the following conferences:

· International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09)

· International Conference on Automation, Robotics and Control Systems (ARCS-09)

· International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09)

· International Conference on Enterprise Information Systems and Web Technologies (EISWT-09)

· International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09)

· International Conference on Information Security and Privacy (ISP-09)

· International Conference on Recent Advances in Information Technology and Applications (RAITA-09)

· International Conference on Software Engineering Theory and Practice (SETP-09)

· International Conference on Theory and Applications of Computational Science (TACS-09)

· International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09)

The website http://www.PromoteResearch.org contains more details.

Sincerely

Walter Jackson

Publicity committee

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Introduction to Bioinformatics - deadline reminder

2009-02-02T13:08:08Z

This is a reminder for those people considering taking our online
course, which begins again in March 2009.

The application deadline is 13 February. However, it is advisable to
apply before the deadline to allow time for any questions in processing
your application.

I have included the course outline below; the full details are on our
website
(http://octette.cs.man.ac.uk/bioinformatics/modules/bs6061.html). If
you have any questions, or need advice on the module options, please
contact Heather.Vincent@...

Week 1 Introduction to distance learning
Bioinformatics as a knowledge-based discipline

Weeks 2 and 3 Introduction to the sequence databases
Quality, redundancy and annotation
Sequence retrieval exercise and group discussion

Weeks 4 and 5 Nucleic acid sequence analysis

Weeks 6 and 7 Independent research and assessment

Weeks 8 and 9 Sequence alignment and database search
1. use of BLAST and FASTA, choosing suitable options;
2. interpretation of the results.

Weeks 10 and 11 Protein function prediction.

Weeks 12 and 13 Protein structure prediction
Practical exercise and group discussion

Weeks 14 to 16 Independent research and work on the second assessment

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

JVMAH: CALL FOR PAPERS

2009-01-29T07:40:56Z

Journal of Veterinary Medicine and Animal Health

www.academicjournals.org/JVMAH

Dear Colleague,

Introducing ''Journal of Veterinary Medicine and Animal Health (JVMAH)"

The Journal of Veterinary Medicine and Animal Health is a multidisciplinary peer-reviewed journal published that will be monthly by Academic Journals (http://www.academicjournals.org/JVMAH). JVMAH is dedicated to increasing the depth of the subject across disciplines with the ultimate aim of expanding knowledge of the subject.

Editors and reviewers

JVMAH is seeking qualified researchers to join its editorial team as editors, subeditors or reviewers. Kindly send your resume to JVMAH@....

Call for Papers

JVMAH will cover all areas of the subject. The journal welcomes the submission of manuscripts that meet the general criteria of significance and scientific excellence, and will publish:

· Original articles in basic and applied research

· Case studies

· Critical reviews, surveys, opinions, commentaries and essays

We invite you to submit your manuscript(s) to JVMAH@... for publication in the Maiden Issue (May 2009). Our objective is to inform authors of the decision on their manuscript(s) within four weeks of submission. Following acceptance, a paper will normally be published in the next issue. Instruction for authors and other details are available on our website; http://www.academicjournals.org/JVMAH/Instruction.htm

JVMAH is an Open Access Journal

One key request of researchers across the world is unrestricted access to research publications. Open access gives a worldwide audience larger than that of any subscription-based journal and thus increases the visibility and impact of published works. It also enhances indexing, retrieval power and eliminates the need for permissions to reproduce and distribute content. JVMAH is fully committed to the Open Access Initiative and will provide free access to all articles as soon as they are published.

Best regards,

Michael Oruah

Editorial Assistant

Journal of Veterinary Medicine and Animal Health.

E-mail: JVMAH@...

http://www.academicjournals.org/JVMAH

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Bioinformatics and Comparative Genome Analysis EMBO course in Hong Kong

2009-01-14T08:29:33Z

Call for application to the :

Bioinformatics and Comparative Genome Analysis course
August 17 - August 29, 2009
HKU-Pasteur Research Centre - Hong Kong

http://www.pasteur.fr/~tekaia/BCGA2009.html

Organizers/Contact:
Roberto Bruzzone, HKU-Pasteur Research Centre - Hong Kong.
Si Lok, Genome Research Center The University of Hong Kong - Hong Kong.
Tin Wee Tan, National University of Singapore - Singapore.
Ueng-Cheng Yang, National Yang-Ming University, Taipei - Taiwan.
Fredj Tekaia, Institut Pasteur Paris - France.

With financial support from:
EMBO - Institut Pasteur Paris.

Aim of the course:

The main objectives of the course are to familiarize young scientists
(Biologists/Computer Scientists/Mathematicians) with bioinformatics
and genome data analysis skills and to encourage multi-disciplinarity
by introducing:

1- advanced fundamental algorithms in bioinformatics,
2- their application in genome analyses,
3- and recent knowledge acquired from genomes studies and perspectives.

The course is aimed for motivated Ph.D and Post-doctoral students, as
well as young assistant professors and junior scientists in Public
Institutions particularly from Asia, Africa and South America, with
background in Mathematics, Statistics, Biology or Computing, who are
involved in Bioinformatics and Genomes studies.

Duration: Full time from August 17 to August 29, 2009.

Location:
Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong
Kong SAR, China.

Accommodation and social: Acceptance to the course includes free
accommodation (double rooms based) breakfast, lunch and dinner.

Application Deadline: April 15, 2009.

More information about the course, how to apply and application form
can be found at the following web page: http://www.pasteur.fr/~tekaia/
BCGA2009.html

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Introduction to Bioinformatics, March 2009

2008-12-29T09:53:05Z

The online course, Introduction to Bioinformatics, from The University
of Manchester, will begin again in March 2009. Like all our distance
courses it is delivered in a Virtual Learning Environment, which allows
us to extend the classroom into the web. We use a range of tools to
support our online teaching activities.

Each course, which is paced to suit those in full-time employment, runs
over 16 teaching weeks.

Teaching and learning are focussed around tutor-supported exercises. In
this course, participants work together on the interpretation of their
results, before receiving feedback from the course tutor. Participants
who wish to be assessed for credits at Masters level should complete
additional independent research for assessment.

Week 1 Introduction to distance learning
Bioinformatics as a knowledge-based discipline

Weeks 2 and 3 Introduction to the sequence databases
Quality, redundancy and annotation
Sequence retrieval exercise and group discussion

Weeks 4 and 5 Nucleic acid sequence analysis

Weeks 6 and 7 Independent research and assessment

Weeks 8 and 9 Sequence alignment and database search
1. use of BLAST and FASTA, choosing suitable options;
2. interpretation of the results.

Weeks 10 and 11 Protein function prediction.

Weeks 12 and 13 Protein structure prediction
Practical exercise and group discussion

Weeks 14 to 16 Independent research and work on the second assessment

You will find information on all our courses, including fees and a link
to the online application form, here :
http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any
questions, or need advice on the module options, please contact
Heather.Vincent@...

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

RE: [Info-gcg] Other: Re - GCG non-support

2008-12-11T07:28:30Z

I've heard that the legal cost is a measly $70,000.
Can we find 70 people to put up $1000?
Or 140 to put up $500?
Or........

Accelrys is being very wimpy about this;
They should give the thing away and let the chips fall where they may.

Nickolas G. Staffa, Jr. Ph.D.
Telephone: 919-316-4569 (NIEHS: 6-4569)
Scientific Computing Support Group
NIEHS E-WITS Contract
National Institute of Environmental Health Sciences
National Institutes of Health
Research Triangle Park, North Carolina

> -----Original Message-----
> From: Steve Thompson [mailto:stevet@...]
> Sent: Monday, November 03, 2008 3:56 PM
> To: Peter Rice
> Cc: mol-evol@...; evoldir@...;
> bio-soft@...; info-gcg@...;
comp-
> bio@...
> Subject: [Info-gcg] Other: Re - GCG non-support
>
> Hi Peter -
>
> I'm picking back up on an old thread from summer 2007 re. the Acclerys
GCG
> 'retirement.' Since that time several developments, only a few
positive

> in my opinion, have clarified the situation.
>
> One - my online petition at www.petitiononline.com was very successful
> (http://bio.fsu.edu/~stevet/Accelrys_petition.pdf) in gathering
> signatures, almost 200 in a month, and in fostering international
> exposure, as the BioInform article from April 2008 attests
> (http://bio.fsu.edu/~stevet/BioInformGCG.pdf). But Accelrys remains
> committed to not releasing any GCG code, due to exhorbiant and without
> profit legal expense. So be it and understood - we tried.
>
> Two - Accelryrs did distirbute the 'perpetual' licenses to all valid
> license holders that were entitled to it, as I announced in this forum
> April 2008, and they worked great, even across multiple nodes in a
> cluster. Thany you Accelrys. However . . .
>
> Three - We (FSU) upgraded our Linux cluster that supports GCG and many
> other bioinformatics tools to CentOS version 5. Unfortunately, almost
> half of the GCG package now fails due to unresolvable library

conflicts
> (as I warned would happen - unfortunately sooner than I had hoped).
Our
> systems operations folk initially thought they could fix this but the
> solution has remained ellusive. The affected programs are all the
oldest
> 'legacy' programs in the package, although some longtime GCG pragrams
like
> Pearson's FastA package remain viable.
>
> Four - SeqLab continues to operate just fine, but without access to
many
> of the analytic tools of the package, its usefullness is quite
impacted,
> though I still think it's one of the best multiple sequence alignment
> editors around. This is where you come back in Peter. It may seem
odd to
> ask, but the need is actually larger now that so much of the package
no
> longer works in an Enterprise (or CentOS) Linux version 5 environment.
> I'm sure that I am not alone in this situation. So here goes - I've
asked
> it many time before, and I've begun to do the work myself starting
with

> PlotCon, but has anybody built SeqLab extension configuration files to
> launch EMBOSS programs?
>
> Cheers - Steve
> Steven M. Thompson
> A C T G stevet@...
> \-/
> http://bio.fsu.edu/~stevet/cv.html
> /\
> /--| FSU SCS / BioInfo 4U
> /---/
> |--/ Florida State University

School

> of
> \-/ Computational Science
> /\
> /--\ 1st floor DIRAC 150G
> |---\ Tallahassee, Florida
> \---\ 32306-4120
> \--| 850-644-4490
> \-/
> /\ 2538 Winnwood Circle
> /--\ Valdosta, Georgia
> /---| 31601-7953
> |--/ 229-249-9751
>
> _______________________________________________
> Info-gcg mailing list
> Info-gcg@...
> http://www.bio.net/biomail/listinfo/info-gcg

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Re: Comparing distances for two trees

2008-11-18T08:52:09Z

Last year, we published(*) a new software to compare phylogenetic trees that may be useful for your project. The program is called TOPD/FMTS and it's freely available at http://genomes.urv.cat/topd.

(*) Puigbo P, Garcia-Vallve S, McInerney JO. Bioinformatics, 2007. 23:1556-1558.

2008/11/18 <areitzel@...>

I am interested in comparing phylogenetic distances between two trees. The two
trees are likelihood trees for different proteins, but each tree has the same
taxa to facilitate pairwise comparisons. I was hoping someone could give me
some advice on how to compare these two distance matrices. The trees do not
have the same topology so the order of the taxa varies between the distance
matrices for the two proteins. The goal for this project is to test for
co-evolution of the two proteins via regression. Thanks in advance for any
assistance.

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Comparing distances for two trees

2008-11-18T06:31:28Z

I am interested in comparing phylogenetic distances between two trees. The two
trees are likelihood trees for different proteins, but each tree has the same
taxa to facilitate pairwise comparisons. I was hoping someone could give me
some advice on how to compare these two distance matrices. The trees do not
have the same topology so the order of the taxa varies between the distance
matrices for the two proteins. The goal for this project is to test for
co-evolution of the two proteins via regression. Thanks in advance for any
assistance.

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

asking phd studentship

2008-11-16T08:48:39Z

Dear Sir/ Madam

I am an Ethiopian citizen currently working in higher institution called Mekella University as lecturer. I would like to enquire PHD scholarship grant. My proposal is Peri-urban biodiversity management: wildlife around Mekelle University, with a focus on the top predator spotted hyena. Would you pleas help me in getting this opportunity.

Thanks in advance for your email.

Best wishes for you

Yours Gidey Yirga

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Other: Re - GCG non-support

2008-11-03T12:56:23Z

Hi Peter -

I'm picking back up on an old thread from summer 2007 re. the Acclerys GCG
'retirement.' Since that time several developments, only a few positive
in my opinion, have clarified the situation.

One - my online petition at www.petitiononline.com was very successful
(http://bio.fsu.edu/~stevet/Accelrys_petition.pdf) in gathering
signatures, almost 200 in a month, and in fostering international
exposure, as the BioInform article from April 2008 attests
(http://bio.fsu.edu/~stevet/BioInformGCG.pdf). But Accelrys remains
committed to not releasing any GCG code, due to exhorbiant and without
profit legal expense. So be it and understood - we tried.

Two - Accelryrs did distirbute the 'perpetual' licenses to all valid
license holders that were entitled to it, as I announced in this forum
April 2008, and they worked great, even across multiple nodes in a
cluster. Thany you Accelrys. However . . .

Three - We (FSU) upgraded our Linux cluster that supports GCG and many
other bioinformatics tools to CentOS version 5. Unfortunately, almost
half of the GCG package now fails due to unresolvable library conflicts
(as I warned would happen - unfortunately sooner than I had hoped). Our
systems operations folk initially thought they could fix this but the
solution has remained ellusive. The affected programs are all the oldest
'legacy' programs in the package, although some longtime GCG pragrams like
Pearson's FastA package remain viable.

Four - SeqLab continues to operate just fine, but without access to many
of the analytic tools of the package, its usefullness is quite impacted,
though I still think it's one of the best multiple sequence alignment
editors around. This is where you come back in Peter. It may seem odd to
ask, but the need is actually larger now that so much of the package no
longer works in an Enterprise (or CentOS) Linux version 5 environment.
I'm sure that I am not alone in this situation. So here goes - I've asked
it many time before, and I've begun to do the work myself starting with
PlotCon, but has anybody built SeqLab extension configuration files to
launch EMBOSS programs?

Cheers - Steve
Steven M. Thompson
A C T G stevet@...
\-/ http://bio.fsu.edu/~stevet/cv.html
/\
/--| FSU SCS / BioInfo 4U
/---/
|--/ Florida State University School of
\-/ Computational Science
/\
/--\ 1st floor DIRAC 150G
|---\ Tallahassee, Florida
\---\ 32306-4120
\--| 850-644-4490
\-/
/\ 2538 Winnwood Circle
/--\ Valdosta, Georgia
/---| 31601-7953
|--/ 229-249-9751

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

'Evolution in Health and Disease' Discussion

2008-10-23T18:52:43Z

Greetings,

This is just to alert you about scientific discussion of a new book:

Evolution in Health and Disease
Edited by Stephen Stearns and Jacob Koella, Oxford University Press, 2008

which has started at our discussion forum:

http://longevity-science.blogspot.com/2008/10/news-evolution-in-health-and-disease.html
Shorter weblink:
http://tinyurl.com/6xyxy5

Comments and suggestions are welcome !

Kind regards,

--------------------------------------------------
-- Leonid Gavrilov, Ph.D.
Website: http://longevity-science.org/
Blog: http://longevity-science.blogspot.com/
My books: http://longevity-science.org/Books.html

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Genetic Algorithms in Search, Optimization, and Machine Learning by Goldberg

2008-09-30T16:19:48Z

Looking for a free version of this book

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

help for PROTDIST similarity and distance matrix

2008-09-23T22:13:41Z

Sir,

Please help me to find amino acid sequence similarity percentage matrix in traingular form(upper/lower) using PRODIST with Dayoff PAM matrix of 60 sequences.Could you please send me some steps and options for finding the required output.

Kinshuk Chandra Nayak

Distributed Information Sub-Centre

Institute of Life Sciences

Department of Biotechnology,

Bhubaneswar-751023,

India

Add more friends to your messenger and enjoy! Invite them now.
_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Theory and Applications in Bioinformatics

2008-09-04T01:14:05Z

Theory and Applications in Bioinformatics is a distance learning course
from the University of Manchester, UK. It will of interest to those who
need to gain confidence in the use of statistics for molecular
evolution. The course covers:

Introduction to Probability and Statistics using Matlab
Traditional Sequence Alignment and Search
Introduction to Probabilistic Sequence Models
Markov Chains and HMM Applications
Phylogenetic Methods

This is a Masters level course, so credits can count towards the MSc in
Bioinformatics.
(http://www.ls.manchester.ac.uk/postgraduate/distancelearning/).

The course is delivered in a Virtual Learning Environment, which allows
us to extend the classroom into the web. Teaching and learning are
focussed around tutor-supported exercises. Additional information is
available here :
http://octette.cs.man.ac.uk/bioinformatics/modules/bs6120.html or from
Heather.Vincent@...

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

primer design tool

2008-06-24T09:48:40Z

Hi everybody!

Does anyone know (and recomend, of course) a free software or a web tool for primer design?

Thanks

Monica

___________________________________
Mônica Paiva Quast
Doutoranda/PhD Student
Laboratório de Macrobentos Marinho
Departamento de Zoologia, IB/UNICAMP - Brazil
+55 19 3521 6347

Gesendet von Yahoo! Mail.
Dem pfiffigeren Posteingang.
_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Re: Bootstrap interpretation

2008-06-10T12:00:10Z

In article <mailman.370.1213016647.3533.mol-evol@...>,
DimitryASuplatov <genesup@...> wrote:

>I want to generate "random" alignment to use it as a neutral evolution
>model for hypothesis testing. I need a phylogenetic tree of my species
>for that.

>I have used phylip package to generate a set of 1000 replicates, then I
>have used PMB model to calculate the distances with protdist and finally
>appllied neighbor and consese with default settings.

>As a result a have an unrooted tree with bootstrap values generaly
>better at the tips than in the center of the tree. In my understanding
>this is a normal case, though some values are equal to 25%.

>So my question is what could I do with this tree? As I understand, 25%
>values emphasize the fact that different parts of distant sequnces do
>not show consistency with overall comparison. I can not crop the
>alignment. Should I use neighbor-joining to calculate the tree directly
>from the alignment?
>Thanks.

I am having trouble understanding what you want to do here. Let me
try to restate it.

If I understand correctly, you would like to simulate random data on
the same tree that generated your species. You are trying to get
this by first making a bootstrap consensus tree of your species, and
then (you don't describe this part) simulating data on that tree.

This won't work, because the bootstrap consensus tree has no branch
lengths, and you need branch lengths to simulate data. The usual
approach is simply to infer the tree from your original data (by
whatever method you prefer) and simulate data on that inferred tree.
While the inferred tree will not be perfect, it should be generally
similar to the unknown true tree and may be good enough for a
neutrality test.

If this is not what you are trying to do, could you restate it?

Mary Kuhner mkkuhner@...

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Bootstrap interpretation

2008-06-09T06:07:30Z

Hello,

I want to generate "random" alignment to use it as a neutral evolution
model for hypothesis testing. I need a phylogenetic tree of my species
for that.

I have used phylip package to generate a set of 1000 replicates, then I
have used PMB model to calculate the distances with protdist and finally
appllied neighbor and consese with default settings.

As a result a have an unrooted tree with bootstrap values generaly
better at the tips than in the center of the tree. In my understanding
this is a normal case, though some values are equal to 25%.

So my question is what could I do with this tree? As I understand, 25%
values emphasize the fact that different parts of distant sequnces do
not show consistency with overall comparison. I can not crop the
alignment. Should I use neighbor-joining to calculate the tree directly
from the alignment?
Thanks.

P.S. I have investigated 43 sequences with average length of 800 aa. The
consese tree is included.

+--------------------------------------------------------------------------------------------------------A4CHA4|A4C
|
|
+------A5V4S1|A5V
|
+---------------------364.0-|
|
| +------Q8VQG6|Q8V
|
|
|
| +------Q83YY8|Q83
|
+295.0-| +--------1000-|
|
| | | +------Q6PWR5|Q6P
|
| | +998.0-|
|
| | | | +------P06875|PAC
|
| | | | +-1000-|
|
+501.0-| +862.0-| +-1000-| +------P07941|PAC
| |
| | |
| |
| | +-------------Q7WZI9|Q7W
| |
| |
| +993.0-|
| +---------------------------A8GGK2|A8G
| | |
|
| | |
+-----------------------------------------A1BBI0|A1B
| +-1000-| |
| | |
+------------------------------------------------A3M5T4|A3M
| | |
| +869.0-| |
+------Q45TR7|Q45
| | |
+-------------------------------------------1000-|
| | |
+------Q60136|PAC
| | |
| +-------443.0-|
+--------------------------------------------------------------Q8CVF4|
Q8C
| | |
| | |
+------A1SES8|A1S
| | |
+-1000-|
| |
+-------------------------------------------------978.0-|
+------A3TPS0|A3T
| |
|
+------| |
+-------------Q8YQA9|Q8Y
| | |
| | |
+-----------------------------------------A8LKU3|A8L
| | |
|
| | |
| +--------------------Q5LRP7|Q5L
| | |
| |
| | |
+504.0-| +624.0-| +------A3SPW1|A3S
| | | |
| | | +936.0-|
| | | |
| | +644.0-| +------A6FNR3|A6F
| | | |
| +848.0-| |
| | +867.0-| |
| | | +-------------A3SAM5|A3S
| | | | +788.0-|
+688.0-| |
| | | | | |
| +---------------------------Q165Q9|Q16
| | | | | |
|
| | | | +-1000-| |
+----------------------------------A3PJP2|A3P
| | | | | | |
| | | | | |
+------------------------------------------------A3JTN7|A3J
| | | | | |
| | | | +481.0-|
+-------------------------------------------------------Q28PW8|Q28
| | | | | |
| | | | | |
+------Q470H7|Q47
| | | | | |
+610.0-|
| | | | +209.0-|
+-------------------------------------------1000-| +------Q0KAF2|
Q0K
| | +-1000-| | | |
|
| | | | | | |
+-------------Q1LN15|Q1L
| | | | | | |
| | | | +429.0-|
+---------------------------------------------------------------------Q1AUI0|Q1A
| | | | |
| | | | |
+------Q67TD9|Q67
| | | | |
+996.0-|
| | | | |
| +------Q8CX57|Q8C
| | | |
+--------------------------------------------------------259.0-|
| | | |
| +------A7NJ94|A7N
| +476.0-| |
+974.0-|
| | |
+------A9B492|A9B
| | |
| | |
+------A0H1F4|A0H
| |
+------------------------------------------------------------------------------1000-|
| |
+------A5USU8|A5U
| |
| |
+------B1LYT1|B1L
| |
+-------997.0-|
| |
| +------Q2CJE9|Q2C
| |
|
|
+----------------------------------------------------------------------922.0-| +------Q0JY93|Q0J
|
| +-1000-|
|
| | +------Q1LBI2|Q1L
|
+995.0-|
|
| +------A1WN00|A1W
|
+-1000-|
|
+------A7CBF7|A7C
|

+---------------------------------------------------------------------------------------------------------------A2RZ58|A2R

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

New conference event for calendar

2008-05-21T03:26:01Z

The Agricultural Biotechnology International Conference is returning to Europe this August and will be hosted by University College Cork in Cork, Ireland. The annual ABIC conference brings many of the world's largest agriculture, fisheries and food biotechnology companies to the host country (many Fortune 500 companies) and this year is no exception.

At ABIC 2008 in Cork, there will be many hot topics under discussion and debate including innovations in areas such as biofuels and bioenergy, animal and plant breeding, fisheries biotech, molecular pharming, dairy and food, including dedicated sessions on policy, regulatory affairs and business strategies. Registration for the conference has now opened and full details of ABIC 2008 are available on the conference website. http://www.abic.ca/abic2008/html/program.html

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Other: another followup (apology)

2008-04-27T17:08:49Z

Hi all -

I would like to offer my apology to Accelrys and its employees for
suggesting that the company would not follow through on their commitment
to supply non-node-locked, non-expiring license keys to all current GCG
custyomers with "perpetual" licenses. As I mentioned in my last posting
Accelrys is now involved in that process and I have received my new key.
It was never my intent to discredit Accelrys, nor its employess. I merely
had not been informed that the process was underway. I am sorry that I
miswrote and hope that any hard feelings can be overcome. Thank you.

Cheers - Steve
Steven M. Thompson
A C T G stevet@...
\-/ http://bio.fsu.edu/~stevet/cv.html
/\
/--| FSU SCS / BioInfo 4U
/---/
|--/ Florida State University School of
\-/ Computational Science
/\
/--\ 1st floor DIRAC 150G
|---\ Tallahassee, Florida
\---\ 32306-4120
\--| 850-644-4490
\-/
/\ 2538 Winnwood Circle
/--\ Valdosta, Georgia
/---| 31601-7953
|--/ 229-249-9751

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Other: followup to Accelrys petition followup

2008-04-25T06:16:28Z

Hello all -

A brief note to let you know what's happened since my posting this last
Wednesday:

Rob Brown of Accelrys did contact me, finally. He says, and I quote:

"The petition and the subsequent BioInform article produced a significant
response and generated inquiries from a number of third party companies
who now wish to discuss various possibilities relating to GCG with us.
We are now in the process of following up on all of those which is taking
some time."

So, it looks like some good has come out of the process, although this
doesn't look like the open source type of arrangement that many of us
hoped for. Regardless, it may mean that the package will not be dying.

And, Accelrys sent me my new non-node-locked, non-expiring license key!

Cheers - Steve
Steven M. Thompson
A C T G stevet@...
\-/ http://bio.fsu.edu/~stevet/cv.html
/\
/--| FSU SCS / BioInfo 4U
/---/
|--/ Florida State University School of
\-/ Computational Science
/\
/--\ 1st floor DIRAC 150G
|---\ Tallahassee, Florida
\---\ 32306-4120
\--| 850-644-4490
\-/
/\ 2538 Winnwood Circle
/--\ Valdosta, Georgia
/---| 31601-7953
|--/ 229-249-9751

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Other: Accelrys petition followup

2008-04-23T10:41:04Z

Hi all - re. http://www.petitiononline.com/gcg/

A huge THANKS to all of you that signed my petition! Within the first
week online I got almost 150 signatures, and John Devereux himself most
recently signed it. I sent Rob Brown of Accelrys an 'official' copy of
the petition and the signatures at the end of last month. However, but
not surprisingly, I have yet to receive one word back from Accelrys. I
realize that we can't force them to do anything, but I at least thought
that they would have the courtesy to respond to it somehow. The petition
did result in a news story though. GenomeWeb News' bioinformatics
newsletter, BioInform, published the story on April 4th. See my copy at:

http://bio.fsu.edu/~stevet/BioInformGCG.pdf

Some may feel that the BioInform story suggests the petition was merely a
means of influencing commercial negotiations with Accelrys regarding code
release, and have nothing to do with public domain availability, but this
was never my objective. It is and remains a plea not to kill the package,
and in particular SeqLab, by whatever means possible, but preferably
within some type of open source arrangement. Furthermore, Accelrys argues
in the article that many more people have signed the petition than
subscribe to the package, and that this somehow invalidates the petition.
This is completely irrelevant as the GCG license has always been to an
institution, allowing as many people in that institution access as wanted,
not to individual investigators. Here at FSU I have supported over 100
GCG users with one GCG license over the years. June should be interesting
for us all. We'll have to see if Accelrys honors their commitment to
those of us with "perpetual" licenses to provide non-node-locked, non-
expiring versions of the license after June 30, 2008. Time will tell.

Cheers - Steve
Steven M. Thompson
A C T G stevet@...
\-/ http://bio.fsu.edu/~stevet/cv.html
/\
/--| FSU SCS / BioInfo 4U
/---/
|--/ Florida State University School of
\-/ Computational Science
/\
/--\ 1st floor DIRAC 150G
|---\ Tallahassee, Florida
\---\ 32306-4120
\--| 850-644-4490
\-/
/\ 2538 Winnwood Circle
/--\ Valdosta, Georgia
/---| 31601-7953
|--/ 229-249-9751

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

GMOD Summer School, Application Deadline April 15

2008-04-09T14:27:24Z

Hello,

This is a reminder that we will start reviewing applications for the
GMOD Summer School one week from today, on Wednesday, April 15. If
you are interested in attending then please submit a statement of
interest by the end of April 15.

See
http://gmod.org/GMOD_Summer_School and
http://gmod.org/GMOD_Summer_School_Statement_of_Interest

for more information.

Please let me know if you have any questions.

Thanks,

Dave Clements
GMOD Help Desk

On Mon, Mar 24, 2008 at 1:32 PM, Dave Clements <clements@...> wrote:

> GMOD Summer School
> 11-13 July, 2008
> National Evolutionary Synthesis Center (NESCent)
> Durham, North Carolina, USA
>
> The first GMOD Summer School (http://gmod.org/GMOD_Summer_School) will
> be held July 11-13, 2008 at the National Evolutionary Synthesis Center
> (NESCent), in Durham, North Carolina, USA. GMOD is a collection of
> interoperable open source software components for managing genomic
> data. GMOD components are used in diverse contexts, with both
> emerging and established model organisms.
>
> The course will provide an overview of GMOD and cover these popular
> components in detail:
> * Chado - a modular and extensible database schema
> * Apollo - genome annotation editor
> * GBrowse - genome viewer
> * CMap - comparative map viewer
> * Community Annotation System - GMOD's most popular components in a
> single system
>
> This is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users
> how to get up and running with popular GMOD components. There will
> also be a concurrent 1 day session aimed at principal investigators
> that will give decision makers an overview of what GMOD can do, how
> the project operates, and what level of resources are needed to use
> GMOD.
>
> The National Evolutionary Synthesis Center (NESCent,
> http://nescent.org) has joined the GMOD project with the goal of
> lowering the barrier to entry for research communities focused on
> emerging model organisms. The GMOD Summer School is a part of this
> effort. NESCent is also extending GMOD components, particularly
> Chado, to better support comparative and evolutionary data.
>
> If you are interested in attending the GMOD Summer School please
> submit a Statement of Interest before April 15, 2008. The course is
> free but enrollment is limited. For application information and a
> tentative program see:
>
> http://gmod.org/GMOD_Summer_School
>
> Please let me know if you have any questions, comments, or requests.
>
> Thanks,
>
> Dave Clements
> GMOD Help Desk
> help@...
> ------------------------
> NESCent offers various courses and workshops, as well as funding
> post-doctoral and sabbatical positions, working groups and other
> meetings. For more information about research and training
> opportunities at NESCent, visit our website at www.nescent.org. Sign
> up for our quarterly electronic newsletter at
> http://www.nescent.org/about/contact.php to automatically receive
> information about events at NESCent.
>

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol

Help with phylogenetic tree construction

2008-03-25T14:18:57Z

Hi,

What I would like to to is to generate a phylogenetic tree based on 16s
sequences from 30 different bacteria plotted onto a larger tree showing
selected organisms from different prominent phyla. The idea is to
display the relationship between my 30 organisms AND how they relate to
the rest of the prokaryotes.

I used to this sort of thing by downloading each sequence from NCBI and
then align them and generate a phylogenetic tree in ClustalW or some
other software. I hope there exist some internet tools now that can do
it all for me, i.e. that I just select the species/strains and the
software retrives the sequences, aligns them and creates the tree
according to mye criteria. Do you know of any such sequences or do
people still do these kind of things "by hand"?

Regards,
Trond Erik

_______________________________________________
Mol-evol mailing list
Mol-evol@...
http://www.bio.net/biomail/listinfo/mol-evol