genscan

[parulvk]

Dear All,

I want to annotate 716Mb of genome in fasta format. However when I run genscan I get following error:

>genscan HumanIso.smat input.fa

reading sequence file input.fa... 838332198 bp

reading parameter file HumanIso.smat... 14 matrices

scoring sequence...
Error : calloc failed on CNCO[strand] array


I get this error since genscan cannot process multiple fasta file. Hence I used http://cpansearch.perl.org/src/CJFIE...run_genscan.pl

This script ran successfully but the output generated were cds,peptide and exon files. However we intend to have our output in gff format.

Any suggestions?

[oxydeepu]

Problem with GenScan.

Dear All,

I want to annotate 716Mb of genome in fasta format. However when I run genscan I get following error:

>genscan HumanIso.smat input.fa

reading sequence file input.fa... 838332198 bp

reading parameter file HumanIso.smat... 14 matrices

scoring sequence...
Error : calloc failed on CNCO[strand] array


I get this error since genscan cannot process multiple fasta file. Hence I used http://cpansearch.perl.org/src/CJFIE...run_genscan.pl

This script ran successfully but the output generated were cds,peptide and exon files. However we intend to have our output in gff format.

Any suggestions?

I Have similiar problem with the genscan predictions. I have an extra doubt, does it give you the 3' UTR of the gene prediction?

Thank you in advance,
Best Regards,
Deepak