[GenoMax]

anybody have good and new version manual send to me

Command line manual from NCBI is linked in post #4.

[skbrimer]

I do not think they got an error. When I run the code I get back the qcovs value and its a number value. I think that they are asking for the hsp_middleline value that shows where the protein and matches and doesn't. The only way I know how to get that is in the xml format and then you either have to cut and paste it from there or have a scritp to extract it from the file. Which is out of m relm of ability, Maybe GenoMax knows how to do that from the standalone BLAST but I have not done it before, other then just using the xml format option.

[kulandaisamy]

anybody have good and new version manual send to me

[kulandaisamy]

Finally got it .heartly thankyou to all

[GenoMax]

Was there an error? Post that.

[kulandaisamy]

i tried but i didn't get it.give me some example.

[GenoMax]

Don't use the -remote option if you are using blast locally.

[kulandaisamy]

ok..thnk you

[GenoMax]

You are running blast+. Not the latest (v. 2.2.30) but close enough. Use @skbrimer's suggestion for the command above.

[kulandaisamy]

blastp: 2.2.28+
Package: blast 2.2.28, build Jun 3 2013 11:32:37

[GenoMax]

What version of blast are you running?

$ blastp -version

[kulandaisamy]

ok.i tried to install blast+.but i didn't get it

[skbrimer]

blastall -p blastp -i plas_3d7.fasta -d approved_target.fasta -m 8 > blas.tab

I'm not sure how you would run the search in the older version of BLAST, NCBI recommends you download the new BLAST+ here is a link to a discussion https://www.biostars.org/p/9480/

I have only used the newer version so the line of code would look something like....

blastp -db nr -query plas_3d7.fasta -query_loc approved_target.fasta -out blas.tab -outfmt "6 qgi sgi qcovs" -remote

Or something to this effect, I'm not sure what the -d flag is on the blastall version of blast but hopefully this can get you pointed in the right direction.

[kulandaisamy]

how to use -qcovs flag in blastp?

[kulandaisamy]

blastall -p blastp -i plas_3d7.fasta -d approved_target.fasta -m 8 > blas.tab

my output file contaiing only Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score.
i want query coverage results