Question: How to prevent blastp from aligning small parts of query sequence and scoring that high?
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gravatar for hodayabeer
18 months ago by
hodayabeer10
hodayabeer10 wrote:

Hi, I was blasting proteome of yeast against a large database of Archaea. Something is wrong with the results because I got too large P Identity for too much proteins. I assume that the problem is that blast scores small parts of the query sequence once it found an alignment to that, and therefore gives good scores even though most of the query sequence doesn't match. How can prevent blast from giving me small alignments? maybe setting the window_size parameter? or normalizing the bitScore with the query length? does hsps have to do something with that? Thanx soo much!

blast sequence alignment • 609 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by hodayabeer10

Can you give an example?

You can screen for results with lower p-value, coverage or identity (using tabular format output)

ADD REPLYlink written 18 months ago by Asaf5.5k

but I want to get only full alignments of the query sequence

ADD REPLYlink written 18 months ago by hodayabeer10

if you are getting the BLAST output in the tabular format then you can get it display alignment length and parse the output for preferred alignment length.

ADD REPLYlink written 18 months ago by Sej Modha4.1k

how can I extract only the results where the alignment lengths is equal or close to the query / subject length?

ADD REPLYlink written 18 months ago by hodayabeer10

It's called glocal mode (global-local), unfortunately not implemented in BLAST.

ADD REPLYlink written 18 months ago by Asaf5.5k

how can I extract only the results where the alignment lengths is equal or close to the query / subject length?

ADD REPLYlink written 18 months ago by hodayabeer10

Output the results in tabular mode (-outfmt 6) and then filter using awk/excel/R etc.

ADD REPLYlink written 18 months ago by Asaf5.5k
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