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 ?