Need help : How can I get the Emboss sixpack output in GFF file

Question

[shiv]

Hi,

I have a genome sequence in Fasta format and I want to perform the Emboss Sixpack tool to get all ORFs (open reading frames) by command-line option. I need the output in GFF/GFF3 format, but every time I am getting the output only in Fasta format. Can anyone help me to sixpack's output in a feature table(GFF/GFF3)?

Thanks in advance

[Mark]

I think if you specify -osformat gff it will output in the format you request. See the manual:

http://bio.biomedicine.gu.se/cgi-bin/emboss/help/sixpack under Output file format

[shiv]

Hi,

Thank you for the quick response. I was specifying -offormat gff and getting the output in Fasta format only. Your suggestion worked for me. :)

[shiv]

hi, How can I get the strand (+/-) information where ORFs originated by using EMboss sixpack? I want to get full GFF or GTF like feature tables for each ORF. Just to clarify, My aim to predict all ORFs in that genome Fasta and then remove the ORFs sequences which are overlapped with the annotated region on the same strand (I have an annotated feature file in GFF format) and keep only those ORFs which are not overlapping with the annotated region(co-ordinates). It would be great if anyone can help me with this.

[Mark]

The gff should contain this information, the start position will be smaller than the end position. eg:

V00294_3 [465 - 49] (REVERSE SENSE) E. coli laci gene (codes for the lac repressor).

It's all in the manual.

[shiv]

This type of output can get from the Emboss getORF package.