ORF translation of a huge number of DNA sequences

Question

[l.souza]

I'm looking for a software which I can translate the open reading frame of a lot of sequences at the same time. I've tried to use EMBOSS Sixpack, but even in the local software there's a limit of sequences to input. What can I use?

[st.ph.n]

Do you have to extract the ORF, or your dna sequences are ATG-STOP already? Eitherway, Biopython can make quick work of it. Also, see this post.

[l.souza]

I need to extract the ORF! Can I do this with Biopython?

[st.ph.n]

You will need to know a little more about your sequences. Are the ORFs in the forward or reverse direction? If reverse, you'll need to take the reverse complement, and then find 'ATG' in a window search of 3 nucleotides. Do you happen to know the approximate length of the ORFs? You will have to then search for stop codons. With finding 'ATG', you can then translate in the forward direction from the first position.

[l.souza]

They are in the forward direction. They have something about 7000nt.

[Pierre Lindenbaum]

see Emboss sixpack replacement : download & install the standalone version.

Answer 1

[h.mon]

You can split your file into smaller files with GenomeTools (gt splitfasta -numfiles 60 seqs.fasta), faSplit by Jim Kent or fasta-splitter by Kirill Kryukov, then loop or parallel through the files.

[l.souza]

Sorry, but I don't understand why I should split my files into smaller ones...

[h.mon]

but even in the local software there's a limit of sequences to input

[l.souza]

I mean a limit in the number of sequences.

[h.mon]

fasta-splitter and faSplit can split by number of sequences.

I thought gt could split by number of sequences, apparently it can't.

[l.souza]

I'm gonna try it... But I would be glad if I'd find something to run all at once.