| Name : biopython
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| Version : 1.30
| Vendor : BioRPMS http://apt_bea_ki_se/
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| Release : 2.bio.fc3
| Date : 2004-11-23 15:33:35
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| Group : Applications/Scientific
| Source RPM : biopython-1.30-2.bio.fc3.src.rpm
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| Size : 8.76 MB
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| Packager : Bent Terp < Bent_Terp_bea_ki_se>
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| Summary : freely available Python tools for computational molecular biology
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Description :
The main biopython releases have lots of functionality, including:
* The ability to parse bioinformatics files into python utilizable data structures, including support for the following formats:
o Blast output -- both from standalone and WWW Blast
o Clustalw
o FASTA
o GenBank
o PubMed and Medline
o Expasy files, like Enzyme, Prodoc and Prosite
o SCOP, including \'dom\' and \'lin\' files
o Rebase
o UniGene
o SwissProt
* Files in the supported formats can be iterated over record by record or indexed and accessed via a Dictionary interface.
* Code to deal with popular on-line bioinformatics destinations such as:
o NCBI -- Blast, Entrez and PubMed services
o Expasy -- Prodoc and Prosite entries
* Interfaces to common bioinformatics programs such as:
o Standalone Blast from NCBI
o Clustalw alignment program.
* A standard sequence class that deals with sequences, ids on sequences, and sequence features.
* Tools for performing common operations on sequences, such as translation, transcription and weight calculations.
* Code to perform classification of data using k Nearest Neighbors, Naive Bayes or Support Vector Machines.
* Code for dealing with alignments, including a standard way to create and deal with substitution matrices.
* Code making it easy to split up parallelizable tasks into separate processes.
* GUI-based programs to do basic sequence manipulations, translations, BLASTing, etc.
* Extensive documentation and help with using the modules, including this file, on-line wiki documentation, the web site, and the mailing list.
* Integration with other languages, including the Bioperl and Biojava projects, using the BioCorba interface standard (available with the biopython-corba module).
We hope this gives you plenty of reasons to download and start using Biopython!
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