Nabble - Bio.net - Autoseq

Re: Re: Genotyper and Windows 2000

2009-11-03T06:34:58Z

Hi,
you can try KernelEx extension from http://sourceforge.net/projects/kernelex/files/ .
That is an evil thing to help you run Win2000/WinXP apps on Win98 or WinME
and I believe you can go the opposite direction. Just install the application,
right-click over the Genotyper program icon, go into Properties and select the
operating system mode under which it should be executed.
As I said, perfect way to run newer apps (like Firefox, some antivirus software)
on Win98/Me ... You have fast computer and all apps you need.
Martin

Phillip San Miguel wrote:

> Miguel Angel González wrote:
>> Dear Lynn Petukhova,
>>
>> I have just see your question about Genotyper software and Windows XP
>> in a
>> web forum. Could you say me how could you run Genotyper in Windows Xp
>> system, please?
>>
>>
>> Thank in advance,
>>
>> Miguel Angel
>
> Hi Miguel,
> I don't know whether Lynn Petukhova still follows this forum after her
> 2002 response to a post "Genotyper and Windows 2000". If no one here has
> run Genotyper under XP, maybe someone on the ABRF forum will have.
>
> Some things you might try: if you run on Vista, you can right-click and
> run an application as if it were running on an earlier version of the
> operating system. I doubt that will work, but might be worth a shot.
> Another possibility is to install a virtual machine running an earlier
> version of windows on your current machine. I have never done this, but
> it might be worth a shot. Finally, Applied Biosystems does have a free
> application "Peak Scanner", that might do at least part of what you
> wanted to do with Genotyper.
>
> Good Luck,

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Re: Genotyper and Windows 2000

2009-10-29T04:28:59Z

Miguel Angel González wrote:

> Dear Lynn Petukhova,
>
> I have just see your question about Genotyper software and Windows XP in a
> web forum. Could you say me how could you run Genotyper in Windows Xp
> system, please?
>
>
> Thank in advance,
>
> Miguel Angel

Hi Miguel,
I don't know whether Lynn Petukhova still follows this forum after her
2002 response to a post "Genotyper and Windows 2000". If no one here has
run Genotyper under XP, maybe someone on the ABRF forum will have.

Some things you might try: if you run on Vista, you can right-click and
run an application as if it were running on an earlier version of the
operating system. I doubt that will work, but might be worth a shot.
Another possibility is to install a virtual machine running an earlier
version of windows on your current machine. I have never done this, but
it might be worth a shot. Finally, Applied Biosystems does have a free
application "Peak Scanner", that might do at least part of what you
wanted to do with Genotyper.

Good Luck,

--
Phillip

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Genotyper and Windows 2000

2009-10-28T09:19:14Z

Dear Lynn Petukhova,

I have just see your question about Genotyper software and Windows XP in a
web forum. Could you say me how could you run Genotyper in Windows Xp
system, please?

Thank in advance,

Miguel Angel

Dr. Miguel Angel González Pérez
Departamento de Biología
Universidad de Las Palmas de Gran Canaria
Campus Universitario de Tafira
35017 Las Palmas de Gran Canaria
Canary Islands
Spain
Phone: (+34) 928 454 543
Fax: (+34) 928 452 922

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Re: quality scores using consed/phrap/phred

2009-10-22T09:36:07Z

Sampson, Joshua (NIH/NCI) [E] wrote:

> Let me open with the standard disclaimor that I'm new to these packages and therefore apologize if i'm submitting an obvious question.
>
> I have received a set off .SFF files that I would like to process/align.
>
> Running consed gives me an .ace file with fragments and their starting points in the reference sequence. This is great.
>
> However, I would also like the quality score for every base in every fragment (not just the consensus sequence). If I had chromat files, I could see how to do this with Phred. However, all I have is the .SFF files. Any suggestions on how to get the Phred Quality Scores for the fragements?
>
> Any help would be greatly appreciated.
>
> Josh
>

Hi Joshua,
sff files are generated by a Roche 454 sequencer. Fasta and qual info
can be extracted from them using sffinfo -- a program Roche provides.

Use sffinfo -h to get the documentation.
--
Phillip

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Re: quality scores using consed/phrap/phred

2009-10-22T09:09:24Z

Hi Joshua,

if you use current consed's add454Reads.perl it's
doing everything for you.

After opening the ace file you can normally work with
your sequences ..

Sorry, I don't see the problem!?

cheers,
Sven

+++ Sampson, Joshua (NIH/NCI) [E] (22.10.2009 16:09):

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quality scores using consed/phrap/phred

2009-10-22T07:09:17Z

Let me open with the standard disclaimor that I'm new to these packages and therefore apologize if i'm submitting an obvious question.

I have received a set off .SFF files that I would like to process/align.

Running consed gives me an .ace file with fragments and their starting points in the reference sequence. This is great.

However, I would also like the quality score for every base in every fragment (not just the consensus sequence). If I had chromat files, I could see how to do this with Phred. However, all I have is the .SFF files. Any suggestions on how to get the Phred Quality Scores for the fragements?

Any help would be greatly appreciated.

Josh

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Fragment analysis--GeneScan Analysis problem

2009-08-06T05:30:39Z

I am returning a refurb ABI 310 to use, primarly for fragment analysis using GeneScan.

No matter what I try, I can't get GeneScan to analyze any peaks past 200 base pairs. If I try to analize with ANY size standard file that is longer than 200 bp the analysis fails.

I've made my own size standard file from Rox500 standard, I've used the default size standards--and the ONLY ones that work are one I made that goes to 200bp (using Rox500 size standard sample to make the file) and the default one on GeneScan that is 120bp.

When I look @ the raw data or the data analyzed with my 200bp size std or the 120 bp size standard, the Rox 500 size standard peaks are there & are just perfect---but it won't size call them and if I try to use any other size standard file it just fails the analysis.

I've even made different analysis parameter files--all of these will work/analize with the two "small" size standard files...but nothing works if I try a size standard bigger than 200.

WHAT TO TRY NEXT?

I also can't get the collection software to start GeneScan and autoanalyze, even though I've told it to in both pieces of software (both GeneScan and Collection should "know" to do this...sigh.) I canlive with this one...no problem to analyze later, but I really need to figure out why I can't size peaks past 200 bp.

Any suggestions would be GREATLY appreciated!

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Need your help in testing mtDNA analysis software product!

2009-08-03T10:26:07Z

Hello Dear Colleagues!
We are currently developing a new automating mtDNA analysis software,
and are in great need in your competent opinion and feedback.
Our team would be really grateful to you, if you could give us some
criticism (or maybe even praise).

The program currently runs under MS Windows OS and requires
Microsoft .net framework 2.0 to be installed on your computer.
It works with *.ab1 files and is doing it quite well (as we hope :) )
If you would be so kind to help in testing - please email me to
mitotyper@... for i could send you a license key, or just post
your email in reply.

Download link is http://rapidshare.com/files/262683748/Mitotyper.msi.html

Thank you very much,
Alexey.

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Re: injection solution which reduces rfu

2009-05-20T04:06:41Z

dna0001@... wrote:

>
> Hi all
> I work in a core lab setting, and have recently upgraded my Applied
> Biosystems 3100 Genetic Analyser to a 3130xl running POP-7. A client wants to
> perform fragment analysis with multiplexed PCR products, but often the peaks of
> interest are off-scale (i.e. > 7000 rfu). To the best of my knowledge, Gene
> Mapper v4.0 and Peak Scanner v1.0 will not analyse these samples due to the
> off-scale peaks. I've tried adding 0.1mM EDTA to the samples (we generally use
> HiDi formamide only for injection), but have found that this can either
> increase or decrease signal strength. Can anyone suggest a solution which will
> decrease signal strength? Will low melting point agarose achieve this? Any
> suggestions would be appreciated.
>
> Many thanks
>
> Oliver
>

Hi Oliver,
You could try reducing the injection time. Or ask your customer to load
less sample.

Seems like adding salt (like EDTA) just competes with product such that
larger fragments diminish in intensity, but smaller ones stay about the
same.
Phillip

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Re: Autoseq Digest, Vol 38, Issue 2

2009-05-19T16:11:09Z

Hi Oliver,
Instead of, or in conjuction with an additive you can dilute the
fragments to get reasonable RFUs. On our 3730 the PCR reactions were
typically diluted 40 to 120 fold. We would titrate a few samples per
marker at 40, 80 and 120 fold, then pick the best dilution for the
rest of the study.
Regards,
Dave

At 01:03 PM 5/19/2009, you wrote:

>Send Autoseq mailing list submissions to
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>
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>When replying, please edit your Subject line so it is more specific
>than "Re: Contents of Autoseq digest..."
>
>
>Today's Topics:
>
> 1. injection solution which reduces rfu (dna0001@...)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 19 May 2009 23:44:33 +0930
>From: dna0001@...
>Subject: [Automated-sequencing] injection solution which reduces rfu
>To: autoseq@...
>Message-ID: <1242742473.4a12bec9391eb@...>
>Content-Type: text/plain; charset=ISO-8859-1
>
>
>
>Hi all
> I work in a core lab setting, and have recently upgraded my Applied
>Biosystems 3100 Genetic Analyser to a 3130xl running POP-7. A client wants to
>perform fragment analysis with multiplexed PCR products, but often
>the peaks of
>interest are off-scale (i.e. > 7000 rfu). To the best of my knowledge, Gene
>Mapper v4.0 and Peak Scanner v1.0 will not analyse these samples due to the
>off-scale peaks. I've tried adding 0.1mM EDTA to the samples (we generally use
>HiDi formamide only for injection), but have found that this can either
>increase or decrease signal strength. Can anyone suggest a solution which will
>decrease signal strength? Will low melting point agarose achieve this? Any
>suggestions would be appreciated.
>
>Many thanks
>
>Oliver
>
>
>
>------------------------------
>
>_______________________________________________
>Autoseq mailing list
>Autoseq@...
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>
>End of Autoseq Digest, Vol 38, Issue 2
>**************************************

________________________________________________________________

David Reynolds
Director
Genomics & Genetics Core
Albert Einstein College of Medicine
Price Center for Genetic and Translational Medicine
Room 419
1301 Morris Park Avenue
Bronx, New York 10461-1602

Tel: (718) 678-1157
Lab: (718) 678-1160
Fax: (718) 678-1016
E-mail: dreynold@...
http://www.aecom.yu.edu/dna/

________________________________________________________________

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injection solution which reduces rfu

2009-05-19T07:14:33Z

Hi all
I work in a core lab setting, and have recently upgraded my Applied
Biosystems 3100 Genetic Analyser to a 3130xl running POP-7. A client wants to
perform fragment analysis with multiplexed PCR products, but often the peaks of
interest are off-scale (i.e. > 7000 rfu). To the best of my knowledge, Gene
Mapper v4.0 and Peak Scanner v1.0 will not analyse these samples due to the
off-scale peaks. I've tried adding 0.1mM EDTA to the samples (we generally use
HiDi formamide only for injection), but have found that this can either
increase or decrease signal strength. Can anyone suggest a solution which will
decrease signal strength? Will low melting point agarose achieve this? Any
suggestions would be appreciated.

Many thanks

Oliver

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Re: Chromas 1.44

2009-05-13T12:09:30Z

Try with FinchTV, it is almost the same
V.

2009/5/13 Jiao, Yuxia <yuxia.jiao@...>

> Hi, there,
>
>
>
> I can't download the Chromas 1.44. Every time I clicked the link
> (http://www.technelysium.com.au/chromas14x.html),it came back with
> "Windows can't display the webpage" . do you have another link that I
> try?
>
>
>
> Thank you very much
>
>
>
> Yuxia
>
>
>
> _______________________________________________
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>
>

--
________________________________________
Dra. Valeria Tekiel

Instituto de Investigaciones Biotecnologicas, UNSAM-Conicet
Av. Gral Paz 5445, Predio INTI; Edificio 19
B1650 KNA San Martin, Buenos Aires. Argentina

TE : 5411 4580 7255-57 (int: 332);
FAX: 5411 4752 9639
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Chromas 1.44

2009-05-13T10:47:46Z

Hi, there,

I can't download the Chromas 1.44. Every time I clicked the link
(http://www.technelysium.com.au/chromas14x.html),it came back with
"Windows can't display the webpage" . do you have another link that I
try?

Thank you very much

Yuxia

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Applied Computational Genomics Course

2009-04-04T18:38:23Z

Genome Canada
APPLIED COMPUTATIONAL GENOMICS COURSE (ACGC)
Led by Dr. Brian Fristensky

WESTERN CANADA- JULY 14 TO JULY 20, 2009 -
Calgary, Alberta, Canada

EASTERN CANADA- AUGUST 25 TO AUGUST 31, 2009 -
Montreal, Quebec, Canada

www.gcbioinformatics.ca/training

Since 2003, the ACGC courses have helped laboratory biologists become power users of the latest software tools. Through mastery of fundamental bioinformatics skills, this week-long course enables working biologists to take charge of their data and their projects. The ACGC course utilizes a wide array of popular software, within the context of a portable and comprehensive bioinformatics system.

1. BIRCH (Biological Research Computer Heirarchy) (http://home.cc.umanitoba.ca/~psgendb):

o Provides a complete bioinformatics suite for analysis of sequences, molecular markers, phylogenetic trees, mircoarrays, and data mining and management.

o Automates use of a wide range of programs (for example, BLAST, FASTA, clustalw, Phylip and many others) through a highly accessible graphic interface.

o Fosters a unique environment for experimentation with data.

2. The Bluejay genome browser (http://bluejay.ucalgary.ca/)

o Creates a means for visualization of the wealth of information hidden within the complexity of the genomes.

o Permits comparisons of the organization of two or more chromosomes.

o Allows for visualization of hot spots of gene expression.

o Facilitates the annotation of new genomes.

3. Genome Canada Bioinformatics Help Desk (http://gchelpdesk.ualberta.ca/)

o Beginner-level introduction to Perl scripting .

o Gives consultation on bioinformatics problems on a fee-for-service basis.

o Offers a repository of software.

o Provides web tools, including BASys (Bacterial Annotation System), PlasMapper, BacMap CGView and others.

4. BioMoby (http://www.biomoby.org/)

o Automatically discovers web services worldwide that work with almost any kind of biological data.

o Facilitates the learning of Perl Scripts for leveraging web services for maximizing research outcomes.

o Creates high-throughput data pipelines through implementation of the Taverna workbench.

Proficiency with bioinformatics tools raises the bar with success in pure and applied research activity, thesis supervisory roles, publication potential, career placement opportunities, and the viability of funding avenues.

After the course, attendees of the ACGC will have FREE internet access to all the Bioinformatics Platform tools and databases used in this course. All software is also freely downloadable.

Faculty

Faculty for the ACGC include some of the best recognized bioinformaticians from across Canada, including Drs. Christoph Sensen, Brian Fristensky, David Wishart, and Mark Wilkinson. Dr. Christoph Sensen was recently featured in international media for his breakthrough research on degenerative disorders linked to chronic wasting disease (CWD) in elk and Mad Cow Disease. Dr. Mark Wilkinson has recently been profiled in publications from a diverse range of international research organizations such as the Heart and Stroke Foundation of Canada, Microsoft Research, and the National E-Science Centre of the UK for his groundbreaking work into data and knowledge representation in the biological sciences, and in cardiovascular research in particular. Dr. David Wishart has been actively involved in teaching and developing bioinformatics training programs across Canada and the United States for more than 10 years. He has published more than 150 papers on bioinformatics and various "omics!
" technologies. Dr. Fristensky has been a contributor to the fields of bioinformatics and plant molecular biology since the early 1980's. Publications span a range of interests, including resistance to biotic and abiotic stress in crops, software for DNA and protein sequence analysis, management of biological databases, and improving software usability in bioinformatics.

Registration and further information

Early Bird enrolment in the week-long course extends now to June 1, 2009 for the Calgary course and to July 1, 2009 for the Montreal course, at a reduced fee of $1,250 Cdn. for Canadian participants and $1,500 Cdn. for international participants.

To register, and for further information, please visit our website at www.gcbioinformatics.ca/training

Enquiries can be made to Susanne Cardwell in Canada at 403-210-6661, email smcardwe@...

Also, it would be greatly appreciated by BIP if you would consider sending out this message to your mailing lists and/or posting the information on your websites (a sponsorship agreement can be arranged for interested parties).

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Re: phrap contig , apply contig quality values?

2009-02-25T04:37:05Z

Umanga wrote:

> Greetings all,
> Firstof all, come from Computer science background ,so I have very little
> knowledge in Bioinformatics.
> Now my question ;
> I assemble AB1 files using phred/phrap.I noticed that after assembling using
> 'phrap', it generates contig file (say 'seq.contigs') and a contig-quality
> file ('seq.contigs.qual').
>
> Now,I want to get the same contig which generated by ChromasPro using phrap.
>
> I noticed that ,if I ignore the config bases with quality value '0' (which
> stored in seq.contigs.qual) , I can get almost same sequence as ChromasPro.
> Is this correct?
> This there a parameter to do this in 'phrap' itself?
>
> Thanks in advance,
> Umanga

Hi Umanga,
Yes, you should remove the bases with zero quality values from the ends
of phrap contigs. A quality value of zero indicates the base call is
random noise. I usually trim the ends of contigs back until I hit the
first base with a 20 or higher quality value.
I don't know of a method to force phrap to do this. It would be nice.
I've never used Chromas or ChromasPro. But different assembly engines
may produce different contigs from the same data set.
Phillip

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phrap contig ,apply contig quality values?

2009-02-24T22:45:51Z

Greetings all,
Firstof all, come from Computer science background ,so I have very little knowledge in Bioinformatics.
Now my question ;
I assemble AB1 files using phred/phrap.I noticed that after assembling using 'phrap', it generates contig file (say 'seq.contigs') and a contig-quality file ('seq.contigs.qual').

Now,I want to get the same contig which generated by ChromasPro using phrap.

I noticed that ,if I ignore the config bases with quality value '0' (which stored in seq.contigs.qual) , I can get almost same sequence as ChromasPro.
Is this correct?
This there a parameter to do this in 'phrap' itself?

Thanks in advance,
Umanga

BigDye terminator mix

2009-01-28T01:35:23Z

I have a large quantity of BigDye Terminator mix v2.0 (about 10,000
standard reactions (80ml))
that I no longer require. Any takers?

Greg Elgar

--
++++++++++++++++++++++++++++++++++++++++
Greg Elgar PhD
Reader in Functional Genomics
School of Biological and Chemical Sciences
Queen Mary, University of London
Mile End Road, London E1 4NS

http://www.sbcs.qmul.ac.uk/people/greg_elgar.shtml
http://www2.sbcs.qmul.ac.uk/staff/greg_elgar
http://www.biology.qmul.ac.uk/research/staff/elgar/index.htm
http://fugu.biology.qmul.ac.uk
http://condor.fugu.biology.qmul.ac.uk/

Tel: 0207 882 3049
++++++++++++++++++++++++++++++++++++++++

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Independent DNA Sequencer engineer/service tech

2008-12-23T14:26:36Z

I'm looking for a reliable independent DNA Sequencer engineer/service
tech for ABI Prism 3100, ABI 3730xl, etc. Please contact me directly
with info.

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ALf express

2008-11-11T06:11:00Z

Hi,

Im also sequencing PCR-Products using Alf Express.

I clean the PCR-Product from the old primers using the PCR-kit from GE.

This product is used directly without any ss-ends.

Instead of cy5-dATP I have sequencing primers 5labeled with cy5.

The sequencing primer are positioned like a nested PCR-primer a little bit
away from the end of the PCR product.

The sequencing reaction is carried out using the Sequencing-Kit from GE.

If you are interested in the protokoll, please let me know.

Saluti and ciao

Sabine Lautenschläger

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Seminar: Successful Lab Automation at Hinxton Hall

2008-10-21T08:05:44Z

PAA Event Invitation
You are invited to a seminar event at Hinxton Hall, Cambridge on 13th January 2009

View the agenda
http://paa.cgml1.com/processaalz//lz.aspx?p1=059751S2&p=1&cID=0&cValue=1

register your place now
http://paa.cgml1.com/processaalz//lz.aspx?p1=059751S2&w=16&cID=0&cValue=1

Date: 13 January 2009 Venue: Hinxton Hall - Cambridge Time: 10am Start Fee: £40 + VAT

Successful lab automation is key to the success of drug discovery, DNA screening programmes, product development and quality control. This conference introduces many new and exciting developments in European academia and to address the constantly changing needs of industry. The speaker programme features leading academics in laboratory automation and will be of interest to academics and industrialists. Presentations will provide practical insights and detailed case studies by scientists for scientists. Delegates will learn about different approaches to automation which will prove invaluable particularly those planning new automation projects or struggling to get the performance that they require. Accompanying the programme of presentations will be a poster session and exhibition featuring the leading suppliers of automation equipment.

This conference will be of interest to academic scientists, research institutes, biotechnology and pharmaceutical companies working in the field of laboratory automation and high content screening.

Register now to ensure your place
http://paa.cgml1.com/processaalz//lz.aspx?p1=059751S2&w=17&cID=0&cValue=1

Speakers:

Prof Dave Povey
Head of Chemical Sciences Division, Faculty of Health and Medical Sciences, University of Surrey
Teaching the skills for successful automation

Prof Ross King
Department of Computer Science, University of Wales Aberystwyth
The Robot Scientist Project

Dr Robert Weinzierl
Cell and Molecular Biology, Imperial College London
Automation of Complex Procedures in Molecular Biology
Prof Dr Kerstin Thurow
Center for Life Science Automation, Rostock Germany
Actual Challenges for High Throughput Technologies in Research and Development

Prof Julie Frearson
Director of Scottish Hit Discovery Facility, University of Dundee
Hit and Lead Discovery in an Academic Setting

Dr Anthony Davies
Institute of Molecular Medicine,Trinity College Dublin
Automation Strategies for High Content Research at Trinity College Dublin

Dr Malcolm Crook
Director Process Analysis and Automation Ltd, Visiting Reader, Faculty of Health and Medical Sciences, University of Surrey
User Interfaces for University Laboratory Work cells

Process Analysis and Automation Ltd, Fernhill Road, Farnborough, Hampshire, GU52 6HE, UK Tel: +44 1252 37 3000 Fax: +44 1252 37 1922

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TET-labeled markers on a ABI 3130xl

2008-10-21T04:57:44Z

Hi all,

We recently obtained a large quantity of microsatellite markers that we
would need to screen as soon as possible. The problem is that the dye
set of the primers is FAM, HEX and TET and not the usual three-colour
triplet FAM, HEX and NED that works fine with the 3130.

Since getting nearly a hundred of new NED-labeled primers to replace the
TET-ones really isn't an option I was wondering if anyone knows a way to
run TET-labeled markers on an ABI3130? Or is it impossible? I gather we
would need at least a TET-containing spectral calibration kit / matrix
for the procedure to succeed.

I know already that the "flourescent amidite matrix standard kit" for
the 310 system which is found on the ABI web page has the correct
labels, but is incompatible with 3130 due to having multiple peaks.
There also doesn't seem to be any other ready-to-use standards to meet
the criteria. I've asked also the local ABI tech support for an answer,
but they're still yet to provide a working solution.

Any help on the matter would be greatly appreciated,

Yours,

Albert Vallunen

--
J. Albert Vallunen, M.Sc., Graduate student
Laboratory of Genetics, Dept. of Biology
20014 University of Turku, Finland
tel. +358 2 333 7085

Home address:
Valaskalliontie 85
23140 Hietamäki, Finland
tel. +358 40 562 8587

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Re: T3 and T7 primers

2008-10-16T07:16:15Z

Buffet, Eleonore wrote:
[...]

>
> Hi I'm a student having a problem with some
> extra research I am conducting. I have come across numerous definitions
> as to the function(s) of T7 and T3. Could you please provide your expert
> opinion as to which are false?
>
> To transfer a plasmid to other bacteria
>
> Used as a priming site (my personal preference)
>
> Can be used to make ssRNA copies of DNA
>
> A promoter for cloned DNA expression
>
> Viral RNApol promoter

[...]
Hi Eleonore,

Your post is (at least partly) on topic for bionet.genome.autosequencing
so I'll answer.

As a sequencing core facility we are frequently bedeviled by these
promoters being used as sequence priming sites. I don't find T3 to be
much of a problem. But there are many variants of T7. Because some
vectors/constructs use one sequence and other use others, we always ask
what vector is being used before picking a T7 primer.

The problem arises because T7, T3 and SP6 were not originally designed
to be sequence priming sites. Rather they are sites where the RNA
polymerases of these respective phages will bind prior to initiation of
transcription. So, if you look at the T7 genome, you will find that the
T7 site is not perfectly conserved. Apparently T7 RNA polymerase is
forgiving of these minor difference.

However, DNA polymerases nearly always must be primed to function. If
the last base of your primer does not match the last base of the priming
site, the reaction will generally fail. (Here having a "dirty" DNA prep
could actually help. Contaminating nucleases could chew back the priming
oligo so it could be extended. Of course the sequence will likely be of
poor quality in such a situation. But arguably better than nothing.

Anyway, to answer your question... 4 of the 5 possibilities you present
are true. "Viral RNApol promoter" is the best, in my opinion, because it
describes their primary (evolved) function--the other 3 correct answers
are derived characteristics. The answer I can't make fit is "Transfer a
plasmid to another bacterium". Though it wouldn't surprise me if,
somehow, this one could be true also.

Good luck with your "research",

Phillip

PS Yeah, I know it is bad form to answer what is obviously a student
homework assignment. But the traffic in this group is so low I couldn't
resist the temptation.

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T3 and T7 primers

2008-10-16T04:49:03Z

Dear Kenneth,

Hi I'm a student having a problem with some
extra research I am conducting. I have come across numerous definitions
as to the function(s) of T7 and T3. Could you please provide your expert
opinion as to which are false?

To transfer a plasmid to other bacteria

Used as a priming site (my personal preference)

Can be used to make ssRNA copies of DNA

A promoter for cloned DNA expression

Viral RNApol promoter

Again, many thanks for you time and excellent postings online.

Wishing you much Happy sequencing!

Love Eleonore xx

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genemapper4.0 problem

2008-09-26T07:47:03Z

My files were generated by ABI3700. Now I have new version
Genemapper4.0. I can open my raw files with mapper4.0 and save the new
project. But now the problem is that the project cannot be reopened.
The example files in the package can be reopened, only mine cannot.
Who may know why? Some modification I could do with my raw files?

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sequencing

2008-08-22T05:35:53Z

whats the idea of incubating on ice after denaturation with formamide ?
thank u
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DNA Sequence Questions summary

2008-08-22T04:54:05Z

What's the aim of incubation on ice after denaturation with Formamide?

thanks!
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: Chromas for Vista

2008-06-22T01:01:39Z

Hello,

Best regards.

I am interested to use Chromas for my sequence analysis. Just
wondering, do you have the free Chromas program to download
for Vista. If so, what is the link to downoload it.

Cheers,

Dr.Rahman

--
Md.Tanvir Rahman
Assistant Professor, Department of
Microbiology and Hygiene,
Faculty of Veterinary Science,
Bangladesh Agricultural
University, Mymensingh-2202,
Bangladesh.
Tel. +44(0)24-765-31406
Mobile. +07774525890
Fax. +44(0)24-765-23568
E.mail: tanvirahman@...

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377 Gel Image files

2008-06-13T13:39:18Z

is there any software to view and edit 377 gel image files on Windows ?

SK

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Re: 377 base spacing problems

2008-06-09T08:45:38Z

Jason Dobry wrote:
> Did you ever solve your base spacing issue with the old 377 sequencers?
> I'm seeing the exact same thing and cannot figure it out.
> Thanks,
> Jason

Hi Jason,
Which base spacing issue was that?
Phillip
Purdue Genomics Core Facility

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377 base spacing problems

2008-06-07T13:04:23Z

Did you ever solve your base spacing issue with the old 377
sequencers? I'm seeing the exact same thing and cannot figure it out.
Thanks,
Jason
--
Jason Dobry
Sequencing Manager
Amplicon Express
2345 NE Hopkins Court
Pullman, Washington 99163 USA
Tel 1-509-332-8080
Fax 1-509-332-6338
jdobry@...
http://www.amplicon-express.com

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Chromas 1.44

2008-04-21T03:54:51Z

I'm interested your Chromas 1.44 sequence analysis program but I use a
PC MacIntosch.
Is available a version useful for Mac OS-X?
Best regard

PhD Vincenza Nardicchi
Dept. Internal Medicine _ Biochemistry Section
University of Perugia_Italy
Tel. +39 075 585 7488 - 7421
vincenzanardicchi@...

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Sheath flow cells

2008-04-18T07:47:27Z

In response to your post at
http://www.bio.net/bionet/mm/autoseq/2000-October/002022.html, we make
sheath flow cells.

What specs do you need?

We have some standard chips at...

http://www.translume.com/miva/merchant.mvc?Screen=CTGY&Category_Code=YC

Eric Jacobson
Vice President
Translume, Inc.
655 Phoenix Drive
Ann Arbor, MI 48108
Phone: 800-378-3505
Phone: 734-528-6371
Fax: 734-528-6334

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FW: Florennce / Italy Immunology Conference/Deadline Reminder: March 30, 2008

2008-03-17T11:24:23Z

DEADLINE FOR SUBMISSION OF ABSTRACT OR POSTER: MARCH 30th, 2008.

FRONTIERS IN IMMUNOLOGY RESEARCH
2008 INTERNATIONAL CONFERENCE
www.firnweb.com

FLORENCE, ITALY
July 22-26, 2008
Hotel Croce di Malta

The Frontiers in Immunology Research Network (FIRN) invites you to
participate in its 2008 Conference to be held in the Florence, Italy, at
the
Croce di Malta Hotel, July 22-26. The conference welcomes researchers
from
academia, corporations, governments and other organizations.
Participants may present their research findings, display their posters,
participate in roundtables or simply observe. To participate as a
PRESENTER please submit via email and post ABSTRACTS and/or brief
descriptions of POSTERS (of no more than 200 words) along with your
complete details by March 30th, 2008 as follows:

Frontiers in Immunology Research Network (FIRN)
64 Holden Street
Worcester MA 01605-3109
USA
Tel.: 508-852-3937, Fax: 508-595-0089
Email: hkan@...
Web: http://www.firnweb.com

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Solexa Next-gen sequencing group

2008-02-29T09:38:40Z

Hi folks,

I am happy to hear of a discussion group for Solexa issues. I suggest that
anyone with questions or issues regarding any next generation sequencing
technology platform also post their questions or comments on the ABRF
Discussion Forum (http://www.abrf.org/index.cfm/page/discList/listserve.htm).

- George

George Grills
Director of Operations of Core Facilities in the Life Sciences
Director of Advanced Technology Assessment
Life Sciences Core Laboratories Center
Cornell University
139 Biotechnology Bldg.
Ithaca, NY 14853-2703
Tel: (607) 255-9693
E-mail: gsg34@...

>>From: madelaine <<mailto:madelaine@...>madelaine@...>
>>Date: February 25, 2008 3:54:02 PM EST
>>To:
>><mailto:bionet-genome-autosequencing@...>bionet-genome-autosequencing@...
>>Subject: [Automated-sequencing] Solexa Next-gen sequencing group
>>
>>Hi (potential) fellow Solexa users,
>>
>>There's a new google group intending to cover all aspects of the
>>Solexa sequencing platform, so if you've got solexa questions (or
>>answers), please join and participate. Please pass this on to other
>>Solexa users you know.
>>
>><http://groups.google.com/group/solexa>http://groups.google.com/group/solexa
>>
>>Thanks a lot,
>>
>>Madelaine Gogol
>>Programmer Analyst
>>Stowers Institute
>>m...@...

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Post-doc advertisement, MPIZ Cologne/Germany

2008-02-27T06:53:50Z

Dear Madam/Sir,

Please see our advertisement below for a post-doc position at the Max Planck
Institute for Plant Breeding Research in Cologne, Germany. Could you please
forward the announcement to contacts who might be interested in this
position. Thank you.

Kind regards

Birgit Thron

Secretary to Prof Maarten Koornneef

Director, Plant Breeding and Genetics

Max Planck Institute for Plant Breeding Research

Carl-von-Linné-Weg 10

50829 Cologne/Germany

Tel: 0049-221-5062-401

Fax: 0049-221-5062-413

E-mail: <mailto:thron@...> thron@...

www.mpiz-koeln.mpg.de

The Max Planck Institute for Plant Breeding Research (MPIZ) seeks

a post-doctoral scientist

to establish Affymetrix chip hybridizations for different types of array. In
addition the successful applicant will work closely with research groups to
prepare hybridization experiments and analyze the data. The position will be
based in the DNA core facility which houses a DNA sequencing service, robots
for array construction and an Affymetrix chip hybridization station.
Extension of the facility to include massively parallel sequencing
approaches is planned for the next year.

We seek a candidate with a PhD in biology, genetics or a related field.
Previous experience with array hybridizations or other genomics-based
approaches would be an advantage. Very good English skills are required and
German language skills would be advantageous. Payment and benefits are
according to the German TVÖD. The position will initially be limited to two
years with the possibility of a further extension depending on performance.

The Max Planck Institute for Plant Breeding Research (MPIZ) in Cologne
(www.mpiz-koeln.mpg.de) is one of the worlds premier sites committed to
basic research and training in plant science. The institute consists of four
scientific departments, three independent research groups and specialist
support, totalling about 400 staff, including externally funded positions.

The Max Planck Society is an equal opportunity employer.

Please send your detailed application by 28 March 2008 to:

Max Planck Institute

for Plant Breeding Research

Personalverwaltung

Carl-von-Linné-Weg 10

50829 Cologne

Germany

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