What are the best practices when storing sub-sequences in a Fasta file?

Question

[Nico]

Hello,

Assume you have a Fasta file from Genbank with one or more entries. Each header shows the accession number first, and the description second.

Say I want to annotate/extract/store a sub sequence of one or more entries and not lose the association with the main sequence. Is there a standard way of doing this?

My first intuition is to create a fasta file that has headers as:

>{Accession} {Description} {subsequence description}

Is there a better way?

Thanks!

Answer 1

[GenoMax]

No there is no standard way other than the requirement that fasta header line start with a >. You can store anything you want on the header line. Be aware that many programs will drop things after first white space, so if you want the header to be carried forward in entirety then make sure you keep the things connected as a single string.

> {Accession}_{Description}_{subsequence description}