Biopython

A beta release for Biopython 1.51 is now available for download and testing.

In the two months since Biopython 1.50 was released, we have introduced support for writing features in GenBank files using Bio.SeqIO, extended SeqIO’s support for the FASTQ format to include files created by Illumina 1.3+, and added a new set of application wrappers for alignment programs, and made numerous tweaks and bug fixes.

All the new features have been tested by the dev team but it’s possible there are cases that we haven’t been able to foresee and test, especially for the GenBank feature writer (as there as just so many possible odd fuzzy feature locations).

Constructing complicated NCBI Entrez searches can be tricky, but it turns out one of the Entrez Programming Utilities called Entrez EInfo can help.

For example, suppose you want to search for mitochondrial genomes from a given taxa - either just in the Entrez web interface, for use in a script with EFetch.

I knew from past experience about using name[ORGN] in Entrez to search for an organism name - but how would you specify just mitochondria? I actually worked this out from the NCBI help and exploring the Entrez website’s advanced search - but it took a while.

As announced here, any last minute requests to postpone dropping support for Python 2.3 from the next release of Biopython must be posted to the main Biopython mailing list no later than Friday, May 8.

Hi all,

You may have noticed we’re trying out using the wiki for Biopython cookbook entries. It’s a new idea so at the moment there are only a few ‘recipes’ on offer. If you have some tricks you find yourself using time and again to solve a problem why not share them? Similarly, if you find yourself coming up against a problem you can’t seem to solve easily with Biopython’s tools send a message to one of the mailing lists proposing it as a cookbook example and someone just might solve it for you!

Congratulations to Nick Matzke and Eric Talevich who have had Biopython projects accepted for this year’s Google Summer of Code. Both projects were accepted as part of The National Evolutionary Synthesis Center’s (NESCent) involvement as a mentoring organisation with the program.

Nick will spend his summer working on modules that access locality data from biodiversity databases and incorporate this information in biogeographical and phylogenetic analyses ( Nick’s abstract) while Eric will be building a parser for the emerging PhyloXML format for storing and sharing phylogenetic trees ( Eric’s abstract).

We are pleased to announce Biopython release 1.50, featuring some significant additions since Biopython 1.49 was released late last year.

GenomeDiagram by Leighton Pritchard has been integrated into Biopython as the Bio.Graphics.GenomeDiagram module.

A new module Bio.Motif has been added, which is intended to replace the existing Bio.AlignAce and Bio.MEME modules. Also have a look at Bio.SwissProt and Bio.ExPASy and their revised parsers.

As noted in a previous news posting, Bio.SeqIO can now read and write FASTQ and QUAL files used in second generation sequencing work. In connection with this, our SeqRecord object has a new dictionary attribute, letter_annotations, for per-letter-annotation information like sequence quality scores or secondary structure predictions. Also, the SeqRecord object can now be sliced to give a new SeqRecord covering just part of the sequence.

We are pleased to announce a beta release of Biopython 1.50 for public testing. There have been some significant changes since Biopython 1.49 was released late last year.

GenomeDiagram by Leighton Pritchard has been integrated into Biopython as the Bio.Graphics.GenomeDiagram module.

A new module Bio.Motif has been added, which is intended to replace the existing Bio.AlignAce and Bio.MEME modules. Also have a look at Bio.ExPASy and the revised Prosite and Enzyme parsers.

Just to let you all know, Biopython is now on twitter. And in case you missed the OBF announcement last month, so is the O|B|F News feed (and BioPerl). You are welcome to follow us (all) on twitter.

I’d also like to remind people there are news feeds for the Biopython news posts (as RDF, RSS, RSS2, or Atom format). We’re planning to have these automatically echoed onto twitter in future… (update) …and that seems to be working now :)

Those of you doing next generation sequencing may be pleased to know that the next release of Biopython is expected to include support for reading and writing FASTQ and QUAL files within our Bio.SeqIO interface. These formats are used for traditional Sanger capillary sequencing, and Roche 454 sequencing (Roche provide tools to convert from their binary SFF files) with PHRED quality scores. Solexa/Illumina sequencers produce a FASTQ variant where the quality scores are encoded differently, and this is also supported.

An Application Note describing Biopython has recently been accepted for publication in the Oxford Journal Bioinformatics. An advance copy of the Open Access article is available online:

P.J.A. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski and M.J.L. de Hoon (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, doi:10.1093/bioinformatics/btp163