How To Represent Multiple Contigs In Ncbi'S Ptt (Protein Table) Format

Question

[psusa64]

I have an assembly that has a number of contigs and for another program I need the proteins in *.ptt (protein table) format. All the examples that I've seem so far contain only one chromosome so how can I make sure that two genes on two different contigs that start e.g. on position 10 and end on position 1000 are recognized as belonging to these different contigs (since they both have the same stat/stop positions)?

Do I have to add a new header for each contig? Is this at all supported by the format?

Thanks

Answer 1

[Hamish]

From what I can see in the documentation found by a quick Google:

• What Is A .Ptt File And How It Is Created?
• BioPerl Bio::FeatureIO::ptt

It looks like a '.ptt' file can only describe the proteins on a single contig. To handle multiple contigs you either:

• Produce a '.ptt' file per contig
• Use knowledge of the relative positions of the contigs to create a supercontig, where the sizes of the gaps between contigs are estimated and the are represented in the sequence by the required length of 'n'. The coordinates used are then relative to the supercontig, thus giving a consistent view of the sequence and corresponding features.