[Bioperl-l] Access GSS sequences using Bio::DB::GenBank

[Chris Fields]

It looks fine.  As for the databases, you can always get the latest  
databases using a script from bioperl-live, which uses  
Bio::DB::EUtilities to access them directly (scripts/DB_EUtilities/ 
einfo.PLS, which should install as bp_einfo.pl).  (looking at the  
below, what is blastdbinfo?)

cjfields4:DB_EUtilities cjfields$ perl einfo.PLS
pubmed
protein
nucleotide
nuccore
nucgss
nucest
structure
genome
biosystems
blastdbinfo
books
cancerchromosomes
cdd
gap
domains
gene
genomeprj
gensat
geo
gds
homologene
journals
mesh
ncbisearch
nlmcatalog
omia
omim
pepdome
pmc
popset
probe
proteinclusters
pcassay
pccompound
pcsubstance
snp
sra
taxonomy
toolkit
unigene


chris

On Aug 13, 2009, at 1:59 PM, Robert Buels wrote:

> OK, commit 15927 adds some more info about -db options for  
> Bio::DB::Query::GenBank, explicitly mentioning protein, nucleotide,  
> nuccore, nucgss, nucest, and unigene, and including a link to an  
> (XML) page from NCBI that lists inputs that NCBI accepts.
>
> Could somebody who knows more about eUtils than me also review this  
> patch and make corrections if necessary?
>
> Rob
>
> Robert Buels wrote:
>> I think you're looking for the -db => 'nucgss' option.
>> I'll add a better listing of this (undocumented) options to the  
>> Bio::DB::Query::GenBank docs.
>> Rob
>
>
> -- 
> Robert Buels
> Bioinformatics Analyst, Sol Genomics Network
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca, NY  14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu
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