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BioJava

This forum is an archive for the mailing list: biojava-l@lists.open-bio.org (mailing list options). Messages posted here will be sent to this mailing list.

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating sequences, file parsers, DAS client and server suport, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.

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BioJava, Dazzle and Google App Engine (Java version) by Rouilly, Vincent

5

by Andreas Prlic-3

BioJava, Bioperl and R by rabee.a.aa

0

by rabee.a.aa

blast parsing question by Bernd Jagla-2

1

by Andreas Prlic-3

Upper case symbols by Andreas Dräger-2

2

by Andreas Dräger-2

chromatogram question: get confident value of the called base by Thien Nguyen-3

0

by Thien Nguyen-3

visualization by nathan genome

0

by nathan genome

(no subject) by nathan genome

0

by nathan genome

Sequence logo by Andreas Dräger-2

1

by mark.schreiber

SimpleGappedSequence using RichSequence objects by Frederik Decouttere

1

by Richard Holland-6

Re: FASTQ in BioJava, BioRuby (and Biopython, BioPerl & EMBOSS) by Andreas Prlic-3

0

by Andreas Prlic-3

How to parse large Genbank files? by Florian Mittag

6

by Andreas Prlic-3

Issues with taxon table not having taxon_id and ncbi_id equal under biosql schema by Deepak sheoran

0

by Deepak sheoran

Retrieving AUTHOR information from PDB file by Andrew Clegg-2

5

by Andreas Prlic-3

Load Genbank files takes ages by Florian Mittag

4

by Florian Mittag

Koen Bruynseels is out of the office. by koen.bruynseels

0

by koen.bruynseels

Ontology OBO is_a TERMs by malteseunderdog

5

by Florian Mittag

Compile error: unmappable character for encoding UTF-8 by pprun-3

3

by Andreas Dräger-2

Pairwise alignment of protein sequences by DavidWZ

6

by Andreas Dräger-2

Request For Feature: let SimpleNamespace or Namespace be Serializable by pprun-3

3

by Richard Holland-6

How to parse pairwise alignment result string by DavidWZ

1

by Andreas Dräger-2

feature request Sequence Alignment by Andreas Prlic-3

1

by Andreas Dräger-2

Can I get the additional information, such as chromosome number from "source" feature from genbank file? by pprun-3

2

by pprun-3

Koen Bruynseels is out of the office. by koen.bruynseels

0

by koen.bruynseels

visualizing pair alignment to a genome by nathan genome

0

by nathan genome

Assembly data reading by Paolo Pavan-2

0

by Paolo Pavan-2

summary biojava user meeting by Andreas Prlic-3

0

by Andreas Prlic-3

Visit my Netlog profile by 夏伟-2

0

by 夏伟-2

BOSC presentation by Andreas Prlic-3

0

by Andreas Prlic-3

: prob in reading sequence by ranjith kurungadam

1

by Richard Holland-6

Reading a newick format tree file (getTreeAsWeightedJGraphT) generates an ArrayIndexOutOfBoundsException in TreeBlock by malteseunderdog

0

by malteseunderdog

Reading a newick format tree file generates an ArrayIndexOutOfBoundsException (TreeBlock, getTreeAsWeightedJGraphT) by malteseunderdog

0

by malteseunderdog

Re: Simple Question - Creating a Java object by Colosimo, Marc E.

0

by Colosimo, Marc E.

BioJava user meeting at ISMB/BOSC by Andreas Prlic-3

0

by Andreas Prlic-3

Simple Question - Creating a Java object (some form of Tree) from a Newick format file by malteseunderdog

1

by Richard Holland-6

SCF Parser issues with gaps and unread peak values ? by Umanga

2

by Andy Yates-3

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