How Can I Download The Results From An Ncbi Blast Search?

Question

[John]

I'm BLASTing a sequence on NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi#), I see a page of results showing the portions of the sequences that aligned to my search sequence. I now want to download these sequences. However, when I click select all and then "get selected sequences", I am taken to a Genbank page containing the full genomes of the organisms, not just the bits that aligned. how can I download the sequences of just the bits that aligned?

Answer 1

[Anima Mundi]

Hello, you may take a look at this.

Answer 2

[Graslevy]

Hey John, When it takes you to the genebank page, (on the top right corner of the page) click 'send to'. Select file (to download to a file) and select the format (Fasta etc).

[Neilfws]

I'm afraid that won't help; he wants sequences of only the aligned regions from the BLAST output.

Answer 3

[Neilfws]

So far as I am aware, NCBI web BLAST lacks the functionality that you require: "get selected sequences" does what it says, namely fetches the complete sequence of the hit.

To retrieve only the aligned regions, you will need to run BLAST locally and parse the output using one of the many libraries available for that purpose - e.g. Bioperl Bio::SearchIO.