Predict AA sequence from assembled transcripts

Question

[Adrian Pelin]

Hello,

Blastx is very slow these days, I was wondering if there are any tools available out there that take a fasta file with assembled transcripts and find the biggest open reading frame and then convert it to peptide sequence (amino acid sequence).

Basically I just want the coding regions so that I can use blastp, which is much faster. I tried google but I must be searching for the wrong thing.

Adrian

Answer 1

[umer.zeeshan.ijaz]

Just to add to the above comment you can use my shell wrapper for EMBOSS's getorf

http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/getorf.sh

It has the following contents:

#!/bin/bash
less <&0| \
    perl -pe '/^>/?s/^>/\n>/:s/\s*$// if$.>1' | \
    perl -nse 'push @a, $_; @a = @a[@a-2..$#a];
    if ($. % 2 == 0){
        chomp $a[0];
        chomp $a[1];
        $r=qx/getorf -sequence=asis:$a[1] $o -stdout -auto 2>\/dev\/null/;
        $r =~ s/>asis/$a[0]/g;
        print $r}' -- -o=$2 | \
        perl -pe '/^>/?s/^>/\n>/:s/\s*$// if$.>1' | \
        perl -nse 'push @a, $_; @a = @a[@a-2..$#a];
        if ($. % 2 == 0){
            chomp $a[0];
            $a[0]=~/>(.*?) \[(\d+) - (\d+)\]\s*(.*)/g;
            $s=(($4=~y===c)=="0")?"+":"-";
            if($f eq "f"){
                print ">".$1."_".$2."_".$3."_".$s."\n".$a[1]}
            elsif($f eq "t"){
                print $1."\t".$2."\t".$3."\t".$4."\t".$s."\t".$a[1]}}' -- -f=$1

Here is how you can use it:

cat contigs.fasta | ./getorf.sh "f" "-minsize=30 -maxsize=10000" 

Check the usage details at:

http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/emboss.html#getorf.sh

Also check out other shell wrappers for EMBOSS utilities here:

http://userweb.eng.gla.ac.uk/umer.ijaz/bioinformatics/emboss.html

Best Wishes,

Umer

[Adrian Pelin]

This is a really cool script! Thanks!

Answer 2

[Neilfws]

One of the EMBOSS tools such as transeq or getorf will do the translation for you, but you'll need to write or find a bit of code to extract the longest ORF.

Answer 3

[seta]

You can try Transcriptdecoder, it gets your assembly fasta file and gives you longest ORF.