What Are The Important Considerations When Merging Annotations From Separate Contigs Into A Single Sequence?

Question

[Michael Barton]

If I have contigs A, B and C and the annotations for each in a GFF3 file what is the algorithm for merging their annotations when the contigs are merged into the single sequence ABC?

For instance the start, stop coordinates and phase should be incremented accordingly. E.g. The start and stop position for gene x on contig B should be incremented by the length of contig A and the phase should also be updated by A % 3.

What other considerations are there?

[Darked89]

How do you do merging? With some padding of gaps (A-NNN-B---C), or ends are touching (ABC)?

[Michael Barton]

Either case. I'm asking with respect to the scaffold software I'm writing - http://next.gs.

Answer 1

[Darked89]

One problem hard to handle:

large coding exon (or ORF in bacteria) running to the end of contig A (or close to it *) and starting close to the edge of contig B. Lets assume that this was annotated using exonerate and some protein X.

No padding between contigs still does not solve deletion of the part of the exon/ORF.

Semi-accurate padding requires that the number of Ns corresponds to the distance on X between the matches.

• ends of contigs may me bad quality / have indels / contain less conserved parts of protein

[Michael Barton]

Possibly these instances may have to be resolved by manually on a case-by-case basis?