Post #1214363

2026-02-06 11:05 UTC

#Bioinformatics question: I&#39;m looking for an open-source command-line tool that would migrate genbank features. So given a genbank file and an alignment between the genbank sequence and another one, it should adjust the genbank features to their positions in the new sequence. I&#39;m not interested in any closed-source solutions and I cannot imagine there isn&#39;t a free solution to this, but I cannot find anything.

Replies (2)

@pjacock@fediscience.org 2026-02-06 11:30

@zerodivision@fediscience.org How exactly are the alignments defined? Simple offsets that apply to the entire feature (easy) or might potentially there be different shifts within a feature (within introns or worse exons)? For the easy case you might use Biopython (shifting locations by an offset is as simple as adding an integer), but would need some familiarity to setup the plumbings. Could probably handle shifting each exon too (sublocations) but more faff. Shifts in CDS meaning due to alignment gaps would be a right pain.

Open ##2630373
@samnm@mstdn.science 2026-02-06 15:16

@zerodivision@fediscience.org this sounds like you want to do a functional annotation with a reference? Have your heard of the tool GeMoMa? Maybe this might help you, but it needs GFF/GTF files.

Open ##2630376