Hi all
Over the years, I noticed that align.seqs fails to be consistent in treating gaps. In V4, for example, I run align gaps against SILVA (at it some or trimmed to V4) and one can get, on a conserved region, something like
AGCTCC-AATAGCGTATATTAA-AGTT-GT-T-GTGGTTAAAAA-GCTCG
AGCTCC-AATAGCGTATACTAA-TGTT-GT-T-GCAGTTAAAAA-GCTCG
AGCTCC-AATAGCGTATATTAA-AGTT-GT-T-GCGGTTAAAAA-GCTCG
AGCTCC-AATAGCGTATATTAA-AGTT-GT-T-GCGGTTAAAAC-GCTCG
AGCTCC-AATAGCGTATACTAA-TGTT-GT-T-GCAGTTAAAAA-GCTCG
AGCTCC-AATAGCGTATATTAA-GGTT-G–TTGCGGTTAAAAA-GTCCG
AGCTCC-AATAGCGTATATTAA-AGTT-GC-T-GCGGTTAAAAA-GCTCG
AGCTCC-AATAGCGTATACTAA-CGTT-GT-T-GCAGTTAAAAA-GCTCG
AGCTCC-AATAGCGTATATTAA-AGTT-GT-T-GCGGTTAAAAA-GCTCG
AGCTCC-AATAGCGTATACTAA-CGTT-GT-T-GCAGTT-AAAA-GCTCG
AGCTCCAA-TAGCGTATATTAA-AGTT-GT-T-GCGGTTAAAAA-GCTCG
AGCTCC-AATAGCGTATATTAA-AA-TTGT-T-GCGGTTAAAAC-GCTCG
AGCTCC-AATAGCGTATATTAA-AGTT-GT-T-GCGGTT-AAAAAGCTCG
The bold is a place where the aligner decided that the gap moved a bit was better (there are more, but the text editor is having issues accepting more than one bold section… THere are three other events in other gap columns). But looking at all, is clearly a misplacement. Happens both with needleman and gotoh.
Is there any way to mitigate this behavior within mothur? I know this alignment system doesn’t compare between reads, but those mistakes add gaps where they are not, and remove others where there are, and I am worried about the future unique and denoising.