Question: How to specify Cut-off/parameters of sequence identity > 70% and query length > 40% in BLAST command line?
0
gravatar for Dineshkumar K
21 months ago by
Kasaragod, Kerala, India
Dineshkumar K40 wrote:

I have been searching homologues sequences of my target gene families in my concerned genome sequences. I need to search the homologues with a score of > 70% identity and > 40% query length to the target gene families. Is it possible to include these cut-off/parameters in the BLAST command line. Thank you in advance.

ADD COMMENTlink modified 21 months ago by gb1.9k • written 21 months ago by Dineshkumar K40
0
gravatar for gb
21 months ago by
gb1.9k
gb1.9k wrote:
-perc_identity

There is no coverage cutoff parameter, so you need to do that yourself afterwards. (It is called qcovs in de outfmt options)

Here you can find all the parameters: https://www.ncbi.nlm.nih.gov/books/NBK279684/

Or use:

blastn -help
ADD COMMENTlink modified 21 months ago • written 21 months ago by gb1.9k

Thank you gb, if it possible could you please elaborate qcovs in de outfmt options.

ADD REPLYlink modified 21 months ago • written 21 months ago by Dineshkumar K40

I believe there is no filter parameter for that but you can output it and filter it afterwards, these are the option:

qlen means Query sequence length
slen means Subject sequence length
length means Alignment length

EDIT you changed the text of your comment:

qcovs is the percentage of basepairs from your query that is used for the alignment against the target. So with an coverage of 90%, the of your query that is used for the alignment with the target that is 90% of the total amount of basepairs or your query.

ADD REPLYlink modified 21 months ago • written 21 months ago by gb1.9k

hello gb, Can you help me out with this? Whenever I use perc_identity it shows this "Error: (CArgException::eInvalidArg) Unknown argument: "perc_identity", Im using tblastn

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by priyankamowlali0

You sure you use blastn? Also don't forget the dash. You can double check the parameter with the blastn -help command.

EDIT: The error is correct. tblastn does not have such option. https://www.ncbi.nlm.nih.gov/books/NBK279684/

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by gb1.9k

yeah, just checked it, thank you. So, if I have to get the sequences with >=50%, i have to manually check them right?

and just a confirmation pident is used for identity percentage, right?

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by priyankamowlali0
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