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How to get BLASTP output using URL only in XML format?

This is how I am doing it right now

  1. I go to https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
  2. Paste query sequence
  3. Select pdb as database
  4. Select PSI-BLAST as algorithm
  5. Run, wait for results and copy paste required data from results

If there is an XML output using url only, I could easily automate the process. How to make such url?

blast blastp
• 3,157 views • link
updated by Ram Ram • written by lifeh2o • lifeh2o

1 answer

Yes, there is a URL API with XML (see http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node33.html#1056)

See also: How To Build The Correct Blast Url For The Rest Interface

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Thank you. But how do I get the RID as XML? Put does not support FORMAT_TYPE.

• 1 views • link
updated by Ram Ram • written by lifeh2o • lifeh2o

I have tried both OTHER_ADVANCED=-c and OTHER_ADVANCED=-c 7 but it gives error. -c is for PSI-BLAST in url api documentation

Message ID#38 Error: Failed to parse the advanced options string: Failed to process the advanced options string
• 1 views • link
updated by Ram Ram • written by lifeh2o • lifeh2o

Setting I_THRESHOLD value solved it, but the results are not from PSI-BLAST. If I check PSI-BLAST on the first page (which shows as a result of PUT) only than PSI-BLAST runs

• 1 views • link
written by lifeh2o • lifeh2o

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