Question

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

1

Entering edit mode

12.5 years ago

John ▴ 790

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?

blast ncbi genbank alignment • 23k views

ADD COMMENT • link updated 6.0 years ago by Biostar 20 • written 12.5 years ago by John ▴ 790

Ram · Answer 1 · 2011-10-15

2

Entering edit mode

12.5 years ago

Anima Mundi ★ 2.9k

Hello, you may take a look at this.

ADD COMMENT • link updated 4.6 years ago by Ram 43k • written 12.5 years ago by Anima Mundi ★ 2.9k

score 0 · Answer 2 · 2011-10-15

0

Entering edit mode

12.5 years ago

Graslevy ▴ 240

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).

ADD COMMENT • link 12.5 years ago by Graslevy ▴ 240

0

Entering edit mode

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

ADD REPLY • link 12.5 years ago by Neilfws 49k

score 0 · Answer 3 · 2011-10-15

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.