[BiO BB] Retrieve list of GenBank Accession Numbers

Johannes Hüsing tmi0m0 at spi.power.uni-essen.de
Mon Feb 4 04:56:47 EST 2002


I would like to obtain a list of genes on a chromosome ordered by their
pseudo base pair position. A list of this kind is supplied by the
NCBI when you click on "Data as Table View" when in the Map Viewer.

This gives me a list of genes with links. I would like to obtain the 
GenBank accession number which is listed under "Nucleotides" when you
follow the respective link (if an accession number exists, which might
not be the case for some ESTs).

I wrote myself a Perl script to spider through these links and filter out
the accession number. However, this causes a lot of Web traffic. Therefore,
I'd like to know if such a list is already available. I have found something
called gbgen.idx but this list seems to be dated. For example, you read
about a gene named CHL1 in the gene list. When searching gbgen.idx, no
appropriate PRI(mate) gene is found under this entry. Instead, the relevant
accession number is listed under CALL. What I would like to know is: Is
the list used by GenBank to select the gene names available somewhere?

Sorry if this is unrelated to free software. I'd rather post general 
question like these in UseNet but haven't found an appropriate forum 
so far.

Best wishes


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