Question: How To Get Ungapped Sequences From Blast Output?
1
gravatar for Drdiran
7.6 years ago by
Drdiran10
Finland
Drdiran10 wrote:

I am interested in getting ungapped sequence hits (hspsnogap) from blast output, I tried using this:

result_handle = NCBIWWW.qblast("blastp", "nr", record.format("fasta"),expect=10,"hsps_no_gap")
blast_records=NCBIXML.read(result_handle)

but there are still gaps in the sequences.

I would appreciate some hints on how to get ungapped sequences in fasta format from blast output.

biopython blast • 2.7k views
ADD COMMENTlink modified 7.6 years ago by Larry_Parnell16k • written 7.6 years ago by Drdiran10
1
gravatar for Fabian Bull
7.6 years ago by
Fabian Bull1.3k
German
Fabian Bull1.3k wrote:

I am not quiet sure which language you are using but this might help. It states that there is a parameter named: ungapped_alignment. This is probably a boolean value so you should set it to true.

If you are able to make a blast by hand: The blastall program has a parameter -g. For ungapped alignment you should set it to -g F

ADD COMMENTlink written 7.6 years ago by Fabian Bull1.3k
1
gravatar for Larry_Parnell
7.6 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Here are two options that will work:

One option: Set -G and -E to high values. -G is the gap opening penalty and -E is the gap extension penalty.

Second option: Set -g to F, where -g is the binary switch to perform a gapped alignment.

ADD COMMENTlink written 7.6 years ago by Larry_Parnell16k
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