blast command line and online
Hello :
I am trying to run the refseq blastp command
> blastp -query short_test.fa -db human_refseq -num_alignments 1 -matrix pam30 -gapopen 5 -gapextend 2 -evalue 10 -outfmt '6 qseqid sallseqid sseq mismatch pident qlen length evalue bitscore qcovs' -out short_refseq.txt
THis is the query I am running and below is the info of my database which in only human :
> Database: sequence.fasta 113,979 sequences; 76,014,371 total residueDate: Oct 31, 2018 3:28 PM Longest sequence: 35,991 residues
Now my problem is online version gives entirely different result to command line version : Command line finds bitscore of only 43.3 while online version finds 90.6 bitscore and peptide(SELPLQEQNYPAVDSPPSGGGWAGWGSWGK)is matched exactly in online version(SEIPLQEQNYLAVDSPPSGGGWAGWGSWGK ) vs command line (SEIPLQEQNYLAVDSPPS) for the same protein.. for example :
> command line
> SELPLQEQNYPAVDSPPSGGGWAGWGSWGK NP_001337561.1 SEIPLQEQNYLAVDSPPS 2 88.889 30 18 3.85E-06 43.3 60
>
>
>online version maps to exact peptide :
SEIPLQEQNYLAVDSPPSGGGWAGWGSWGK
> Score Expect Identities Positives Gaps
90.6 bits(206) 3e-22 28/30(93%) 28/30(93%) 0/30(0%)
Can anyone help me with parameters ..T
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Are you limiting online search to the same database (human_refseq)? Online
blastpusesBLOSUM62by default.Gap open penalty is 11 and gap extension is 1online. These are all different in your command line search.I tried using gap penalty to 11 and 1 too..bitscore reduced to 33 further with that gap value ..Becuase its short sequence online blastp changes the matrix to pam30 ..
That is good to know. That leaves the database you are using as possible key difference. Are you using the latest v. 2.8.1?
mine is 2.7.1..will that be problem ? I updated the version but still same results.