Question: determining length of fasta cds and protein sequences
gravatar for vigneshprbh37
4.2 years ago by
vigneshprbh3720 wrote:

I have performed blastn and tblastn executions for a list of selected genes. for purpose of analysis i need to compare the best hit alignment length with best percent identity to the actual length of the sequences of cds protein.

is there a bioinformatic tool i can use for accomplishing this


is there any algorithms i can use on linux to accomplish the same

fasta protein cds software • 1.3k views
ADD COMMENTlink modified 4 months ago by Biostar ♦♦ 20 • written 4.2 years ago by vigneshprbh3720
gravatar for lieven.sterck
9 months ago by
VIB, Ghent, Belgium
lieven.sterck4.5k wrote:

Assuming you are using the most recent version of blast (and you should) , you can ask to add the query (or hit) length to be added in certain output formats, such as the tabular one.

you'll need to add the following to your blast cmdline:

-outfmt "6 std qlen slen"

this will add, to the normal output the query input seq length and the hit seq length in the second-to-last and last column respectively .

See the blast help (blastp -help) for more info on those parameters (and how to add others for instance)

ADD COMMENTlink written 9 months ago by lieven.sterck4.5k
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