Error while running pfamscan.pl : Unable to translate nucleotide sequences to protein sequences

Question

[AB]

Hi,

I am trying to find novel lincRNA's. I have sequence data from 4 replicated which was aligned and assembled using STAR and cufflinks. I then filtered out the single exons and I want to run pfamscan on my multiexon.fa file. I tried giving the option -translate to translate my nucleotide sequences to protein before searching PFAM, but I am getting this error

Command 'translate' not found in /usr/local/share/doc/hmmer, /Users/ab34/Downloads/hmmer, /Users/ab34/perl5/bin, /Users/ab34/perl5/perlbrew/bin, /Users/ab34/perl5/perlbrew/perls/perl-5.16.0/bin, /usr/local/bin, /usr/bin, /bin, /usr/sbin, /sbin at Bio/Pfam/Scan/PfamScan.pm line 853.

Did I not install something right ? How should I fix this ?

Thanks

Answer 1

[SES]

The pfamscan script is expecting a program called translate that is/was part of HMMER version 2.3.2. The tricky part is that it is an accessory program so you won't find it in the 'bin' folder after you compile HMMER, it will be in a directory called 'squid'. Your options are:

1. Add the PATH to this 'squid' directory so the program can be found
2. Translate your sequences by another method before running pfamscan (e.g., with EMBOSS getorf or sixpack)

[AB]

I already tried getorf and sixpack but my files were too large. So i wrote a script to translate my fasta file and run it. But i will definitely try adding PATH to the squid directory and see if that works.

Thank you

[SES]

Can you explain what you mean by the files were too large? Also, it would be helpful to show any error messages.

[AB]

Emboss sixpack allows a maximum file size of 10.5MB. My fasta file has 6000 sequences and was larger than that. So i got this error

File upload error: The field upfile exceeds its maximum permitted size of 10485760 bytes.

[SES]

Oh, I see. You are trying to run it on the web server. I suppose you could try splitting your file, or better yet, running it on your local machine (or a cheap cloud instance).

[arunprasanna83]

Can you please explain about the point 1 ?. I had HMMER-3.1b2 and cant find 'squid' folder. How do I find it & add the path ?