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bioinformaticsblastncbi

blast given GI NCBI nucleotide database

I have local database driven website which contains a few sequences which are uniquely identified via their GI number. Is it possible to link to the 'NCBI blast site' directly given the GI. For example the sequence for GI 903049 has this link:

http://www.ncbi.nlm.nih.gov/nuccore/903049

It links to this blast page:

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&QUERY=U22848.1&DATABASE=nr&MEGABLAST=on&BLAST_PROGRAMS=megaBlast&LINK_LOC=nuccore&PAGE_TYPE=BlastSearch

I would like to link to this site directly without having to go to NCBI. Thanks.

Solution

  • you can use ncbi efetch to download all your gis:

    http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=903049&rettype=fasta&retmode=text

    and run a local version of blast: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download

    you can also ask Biostar: http://www.biostars.org/show/questions/