question on exonpart hints
Posted: Thu Nov 19, 2015 7:52 pm
Originally posted in the old forum by Jason on 22.01.2013 - 03:30
Hi again,
Thanks first the quick response as always.
My question is concerning to the hint type "exonpart":
"part of an exon in the biological sense. The bonus applies only
to exons that contain the interval from the hint. Just
overlapping means no bonus at all. The malus applies to every
base of an exon. Therefore the malus for an exon is exponential
in the length of an exon: malus=exonpartmalus^length.
Therefore the malus should be close to 1, e.g. 0.99."
So if I have a manually curated protein from species A and I used scipio to map it against related species B. It turns out that the whole protein (11 exons) is contained in one ORF (no stop codons!) because they have very different exon-intron structure. To my understanding is if I use the 11 exon alignments as ep hints it will increase augustus's chance to predict one gene one exon, and only if I use the 11 exon alignments as exon(or even CDS) hints then it might make augustus to predict one gene multiple exons within one ORF?.
Just want to clarify this - it turns out scipio can be pretty good hints after filtering out the spurious alignments.
Best Wishes,
Jason
Hi again,
Thanks first the quick response as always.
My question is concerning to the hint type "exonpart":
"part of an exon in the biological sense. The bonus applies only
to exons that contain the interval from the hint. Just
overlapping means no bonus at all. The malus applies to every
base of an exon. Therefore the malus for an exon is exponential
in the length of an exon: malus=exonpartmalus^length.
Therefore the malus should be close to 1, e.g. 0.99."
So if I have a manually curated protein from species A and I used scipio to map it against related species B. It turns out that the whole protein (11 exons) is contained in one ORF (no stop codons!) because they have very different exon-intron structure. To my understanding is if I use the 11 exon alignments as ep hints it will increase augustus's chance to predict one gene one exon, and only if I use the 11 exon alignments as exon(or even CDS) hints then it might make augustus to predict one gene multiple exons within one ORF?.
Just want to clarify this - it turns out scipio can be pretty good hints after filtering out the spurious alignments.
Best Wishes,
Jason