Question: How to get BLASTP output using URL only in XML format?
0
gravatar for lifeh2o
4.1 years ago by
lifeh2o0
Pakistan
lifeh2o0 wrote:

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?

blastp blast • 1.4k views
ADD COMMENTlink modified 4.1 years ago by Pierre Lindenbaum113k • written 4.1 years ago by lifeh2o0
2
gravatar for Pierre Lindenbaum
4.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum113k wrote:

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

ADD COMMENTlink written 4.1 years ago by Pierre Lindenbaum113k

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

ADD REPLYlink written 4.1 years ago by lifeh2o0

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

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by lifeh2o0

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

ADD REPLYlink written 4.1 years ago by lifeh2o0
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