[Biopython-dev] Possible Contribution: UCSC Blat and Ensembl SSAHA Sequence Locator

Anthony Metzidis Anthony.Metzidis at ktl.fi
Fri Feb 7 03:43:29 EST 2003

We've developed a Python API for the UCSC 
BLAT(http://genome.ucsc.edu/cgi-bin/hgBlat?command=start) and Ensembl 
SSAHA (http://www.ensembl.org/Homo_sapiens/ssahaview) genome search tools.

Using our tool, you can input a series of dna sequences in Fasta format 
and then get the results back as dictionaries, indexed by the Fasta 
title, of dictionaries indexed by the fields presented by the web 

The http connection and parsing of the HTML results pages are handled by 
our tool.

We use these tools for locating large amounts of SNPs that are not yet 
annotated by the public DBs, or to relocate annotations that reference 
an older genome build to a newer one, for example.

We would like to contribute this to BioPython, if you think there would 
be an interest in it.

If so, could you offer advise about other existing BioPython interfaces 
that we should model ours after?  I would like the interface to be as 
consistent as possible with the rest of BioPython.

Any other advise on making contributions would be greatly appreciated.


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