Question: Extracted orfs or contigs from scaffolding
gravatar for Leandro de Mattos
5.8 years ago by
Leandro de Mattos90 wrote:

Dear, I obtained the scaffold from contigs + pair-end information through of the SSPACE program,  and now I would like to get the contigs extend, and then get the ORFs, which programs could I use? I have the scaffold in Fast format.

Thanks for any help,


extract orfs scaffold • 2.0k views
ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Leandro de Mattos90

What is your data from, genomic DNA or transcripts, prokaryote eukaryote? You most likely have to do a gene-prediction and not simply ORF detection. While ORFs can be easily detected using getOrf, they are mostly useless to predict on eukaryote DNA. Search this site for gene-prediction pipeline, that is what you should apply next.  

I did not get the part about 'extend contigs', because that's what scaffolding already did.

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by Michael Dondrup47k

Hi Michael, my data is  DNA genomic of eukaryote. I used pair-end reads obtained of Illumina for extend  my assembled obtained from 454 sequencing, making the hybrid assembled, as the final results I obtained the scaffolds.  Can I use prediction software such as GLIMMER? I think that theses programs the input data is contigs. I need a program to handle Scaffolds.

Thanks by help,



ADD REPLYlink written 5.8 years ago by Leandro de Mattos90
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