Biopython Tutorial and Cookbook
Biopython Tutorial and Cookbook by Jeff Chang
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