Help With BioPython BLAST Output

Question

[niamshah]

Hi,

I am new to BioPython and am writing a program to BLAST human amino acid sequences. My search query is:

NCBIWWW.qblast(
  program="blastp",
  database="nr",
  sequence=BLASTSeq,
  entrez_query="txid9606[ORGN]",
  matrix_name='BLOSUM62',
  word_size='2',
  expect='10',
  gapcosts='11 1',
  composition_based_statistics='no adjustment')

but the alignment title of the BLAST result looks like:

('sequence:', u'gi|964750848|ref|NP_001304891.1| periodic tryptophan protein 1 homolog isoform 2 [Homo sapiens] >gi|332241720|ref|XP_003270028.1| PREDICTED: periodic tryptophan protein 1 homolog isoform X2 [Nomascus leucogenys] >gi|194382424|dbj|BAG58967.1| unnamed protein product [Homo sapiens]')

I was wondering why the titles include multiple protein names and organisms, and how I can change my code so that my program only returns one human protein.

My full BLAST method is:

def callBLAST (BLASTSeq):
    from Bio.Blast import NCBIWWW
    from Bio.Blast import NCBIXML
    result_handle = NCBIWWW.qblast(program="blastp", database="nr", sequence=BLASTSeq, entrez_query="txid9606[ORGN]", matrix_name='BLOSUM62',word_size='2',expect='10',gapcosts='11 1',composition_based_statistics='no adjustment')
    blast_record = NCBIXML.read(result_handle)
    E_VALUE_THRESH = 0.04
    for alignment in blast_record.alignments:
        for hsp in alignment.hsps:
            if (hsp.expect < E_VALUE_THRESH):
                print('****Alignment****')
                print('sequence:', alignment.title)
        break

Thanks!

Answer 1

[BI0SH0CK3D]

There is an argument in the qblast function called "hitlist_size" described as "Number of hits to return. Default 50."

When looking for one human result I use the arguments "hitlist_size = 1".

For more information, ener this into the intepreter:

from Bio.Blast import NCBIWWW

help(NCBIWWW.qblast)

I also had an issues with multiples names in one excel cell in the output like this:

[RecName: Full=Neuromodulin; AltName: Full=Axonal membrane protein GAP-43; AltName: Full=Growth-associated protein 43; AltName: Full=Neural phosphoprotein B-50; AltName: Full=pp46 >gi|61213904|sp|Q5IS67.1|NEUM_PANTR RecName: Full=Neuromodulin; AltName: Full=Axonal membrane protein GAP-43; AltName: Full=Growth-associated protein 43]

if it still appears with the hit list size of one, there is an excel trick that can help. I highlight the column with the cluttered results and do a search and replace for >*. This will delete anything after the > because * is a wildcard character. This will delete all the extra stuff. I would make sure that there is nothing in them you want first.