[BioPython] BLAST Parser hsp.end
kumar s
ps_python at yahoo.com
Fri Feb 11 13:36:04 EST 2005
Hello all:
I am new to BioPython. I want to parse a gene to human
genome sequence and after a quick surfing of
documentation, I have some basic questions.
1. I took a BLAST output from a local blast. I blaster
a cDNA sequence to Human genome - ref_hs_chr11.fa (
Human genome chromosome 11).
I parsed the blast output and wanted to print the
sbjct Start and Sbjct end.
>From the class diagram in the docs. I do not see the
hsp.sbjct_end.
How can i Print the end of an alignment.
2. Can I BLAST human genome at NCBI by running BLAST
over the internet. In the link provided in the
documentation,
http://www.ncbi.nlm.nih.gov/BLAST/blast_databases.shtml
only some databases are there, how do I choose Human
genome blast.
Eg.
from Bio.Blast import NCBIWWW
b_results = NCBIWWW.blast('blastn', 'nr', f_record)
what should I feed in in the place of nr - for human
genome.
Any ideas.
Thanks
K
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