Biopython Tutorial and Cookbook by Jeff Chang
English | PDF | 2018 | 344 Pages | ISBN : N/A | 2.37 MB
English | PDF | 2018 | 344 Pages | ISBN : N/A | 2.37 MB
Python is an object oriented, interpreted, flexible language that is becoming increasingly popular for scientific computing. Python is easy to learn, has a very clear syntax and can easily be extended with modules written in C, C++ or FORTRAN.
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:
- Blast output - both from standalone and WWW Blast
Clustalw
- FASTA
- GenBank
- PubMed and Medline
- ExPASy files, like Enzyme and Prosite
- SCOP, including 'dom' and 'lin' files
- UniGene
- 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:
NCBI - Blast, Entrez and PubMed services
- ExPASy - Swiss-Prot and Prosite entries, as well as Prosite searches
Interfaces to common bioinformatics programs such as:
Standalone Blast from NCBI
- Clustalw alignment program
- EMBOSS command line tools
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