Entering edit mode
9.6 years ago
lifeh2o
•
0
This is how I am doing it right now
- I go to https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
- Paste query sequence
- Select pdb as database
- Select PSI-BLAST as algorithm
- 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?
Thank you. But how do I get the RID as XML? Put does not support
FORMAT_TYPE
.I have tried both
OTHER_ADVANCED=-c
andOTHER_ADVANCED=-c 7
but it gives error.-c
is for PSI-BLAST in url api documentationSetting 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