[Biopython] Fwd: Qblast : no hits

[Peter]

On Sun, Apr 25, 2010 at 4:24 AM, Karthik Raja wrote:

> *Below given are the code and the traceback. *

Great - I can run that and get the same traceback.

Here is a shorter version which does the same thing - removing all the
parameters you don't actually set:

from Bio.Blast import NCBIWWW
result_handle = NCBIWWW.qblast("blastp", "nr", "SSRVQDGMGLYTARRVR",
entrez_query='(none)', expect=200000, hitlist_size=50,
matrix_name='PAM30', word_size=2, alignments=500, descriptions=500,
format_type='XML')

Getting shorter still:

result_handle = NCBIWWW.qblast("blastp", "nr", "SSRVQDGMGLYTARRVR",
matrix_name='PAM30')

The problem is the matrix name - remove that and the error goes away.
So progress :)

Doing a little digging, this is the error message from the NCBI is:

Message ID#35 Error: Cannot validate the Blast options:  Gap existence
and extension values of 11 and 1 not supported for PAM30
supported values are:
32767, 32767
7, 2
6, 2
5, 2
10, 1
9, 1
8, 1

As I guessed earlier, Biopython needed a little update to recognise
this error message and pass it to the user. I've done that.

In your case, you need to pick gap parameters appropriate for PAM30.

Peter