determining length of fasta cds and protein sequences

Question

[vigneshprbh37]

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

Answer 1

[lieven.sterck]

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)