[Next-Generation Sequencing Book]
  • [Photo] J.W. Bizzaro • March 9, 2001
    Jeffrey Chang writes, ``The 1.00a1 release of Biopython is ready for download. This release marks two milestone in the package. First, it is now 1.00, which means it's relatively feature complete. It has support for sequences & annotations, alignments, substitution matrices, BLAST, ClustalW, ENZYME, FASTA formatting, GenBank, GoBase, Medline, Prosite, Rebase, SCOP, SwissProt, and UniGene. Second, it's the first non-developer's release, which means it's now reasonable to expect people to download it and do work immediately without having to mess around with the code.''

    BioPython:
    http://www.biopython.org

    Ewan Birney writes, ``We are very pleased to announce the Bioperl 0.7 release. This release represents a very significant improvement to the previous 0.6 series and brings a number of important new features to bioperl....Bioperl 0.7 is predominantly the effort of Jason Staijch and Hilmar Lapp who worked to build on top of the Bioperl 0.6 effort. Lorenz Pollack and Peter Schattner also provided significant pieces of code. The effort was supported by general bioperl developers, in particular Ewan Birney and Chris Dadigidan. Many thanks also goes to our Mac (Todd Richmond) and NT (Shelly Mistry) testers.''

    BioPerl:
    http://bio.perl.org
    Test release:
    ftp://bio.perl.org/pub/DIST/bioperl-0.7.0.tar.gz

Discussion forums: Major Releases for BioPython and BioPerl

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Parsing Alternative Splicing Gene information from Genbank file using Bioperl
Submitted by Amrita Visdom ; posted on Monday, July 19, 2010
Hi All, I am a novice programmer in Bioperl. For my project, I have to parse the Genbank files and make a dataset. But I am facing the problem while mapping the mRNA and CDS of the Alternative Splicing genes. Whether there is any special module in Bioperl, which will extract the Alternative Splicing genes from the Genbank file, or how we can parse the Alternative Splicing gene information from the Genbank file using Bioperl. Example of Alternative Splicing gene entry : http://www.ncbi.nlm.nih.gov/nuccore/1145692 Thanks, Amrita

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Hi All, I am a novice programmer in Bioperl. For my project, I have to parse the Genbank files and make a dataset. But I am facing the problem while mapping the mRNA and CDS of the Alternative Splicing genes. Whether there is any special module in Bioperl, which will extract the Alternative Splicing genes from the Genbank file, or how we can parse the Alternative Splicing gene information from the Genbank file using Bioperl. Example of Alternative Splicing gene entry : http://www.ncbi.nlm.nih.gov/nuccore/1145692 Thanks, Amrita

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