[BioC] Batch sequence retrieval

Daniel Brewer daniel.brewer at icr.ac.uk
Mon Jun 18 13:19:58 CEST 2007

Hi all,

I am in a situation where I would like to download all the sequences
associated with human IMAGE clones and then blast them a range of other
sequences (~3.4 million).  I have the accession numbers for all of them.
I have tried a number of ways to do this:
1) Search for "IMAGE: homo sapiens" and download the fasta sequence.
This fails after a while for no reason.
2) A script using getSeq from the annotate library.  This is very slow,
but is chugging a way.
3) The batchentrez utility.  There seems to a problem with the link at
the moment.

Has anyone got any suggestions of a better way to do this.  Does Genbank
allow SQL access?

Many thanks


Daniel Brewer, Ph.D.
Institute of Cancer Research
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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