Daniel Lawson
@VBannotator
Annotating vector genomes one locus at a time. MSA and Apollo screenshots. Tweet any @VectorBase loci that need love. Follow @strumpfe for non-annotation tweets
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Comparison of #Anopheles #gambiae #arabiensis #quadriannulatus. Needs manual curation to tease those ionotropic receptor predictions out. #VBannotation
Still finding merged predictions like this. Chaperonin and 4 ionotropic receptors from #Anopheles #arabiensis. All introns supported by aggregated #RNAseq junction counts. #VBannotation
Gr1 gustatory receptor, 1 novel, 1 split and 1 modification. #Anopheles #gambiae #complex #VBannotation
This is a common feature of many #Anopheles loci (and other mosquitoes) where there is evidence for multiple 5' UTR #alternative isoforms i.e. No change to peptide CDS. Maybe single cell transcriptomics will shine a light but till then is it worth @VectorBase curating these?
Lack of evidence for in-frame introns in 2nd #alternative #isoform and subtle compensatory splice site prediction issue. Appraisal of genome annotation can be about the little things. #MarginalGains #VBannotation
Reviewing old #Anopheles #gambiae predictions and there seems to be a systematic issue with the mis-prediction of in-frame introns. Here's a couple of examples. #VBannotation
5-oxoprolinase. 1 split and 2 edits. Only 2 exons but 1350 aa. Gaps in #coluzzii are in the assembly. #Anopheles #gambiae #complex #VBannotation
LL6, lipopolysaccharide induced TNF alpha transcription factor 6. 3 novel and 5 edits. #melas is partial. #Anopheles #VBannotation
LL5, lipopolysaccharide induced TNF alpha transcription factor 5. 3 novel and 6 edits. Nyssorhynchus are either absent or too far diverged for simple pairwise similarity searches. #Anopheles #VBannotation
LL3, lipopolysaccharide induced TNF alpha transcription factor 3. 6 novel, 2 splits, and 3 edits. #maculatus is partial missing the first exon. #Anopheles #VBannotation
I think you've chosen the wrong ORF there Mr MAKER. Should probably give this a new ID as it has no correspondence to the existing CDS #AnnotationFail #VBannotation
LL2, lipopolysaccharide induced TNF alpha transcription factor 2. 2 novel, 2 edits, and one missing (#maculatus). Short predictions from Nyssorhynchus are prob alternative isoforms i.e. this is not a true reflection of transcript diversity for this locus. #Anopheles #VBannotation
LL2, lipopolysaccharide induced TNF alpha transcription factor 2. 1 novel, 2 edits. #Glossina #VBannotation
LL1, lipopolysaccharide induced TNF alpha transcription factor 1. 1 novel, 2 edits. Partial prediction for the usual suspects #christyi & #maculatus. #Anopheles #VBannotation
Osi10, protein osiris 10. 1 novel, 12 splits, 3 edits and one locus split over scaffolds (maculatus). 2 loci are partial (darlingi & maculatus). #Anopheles #VBannotation
Osi4, protein osiris 4, 1 novel, 4 edits. #Glossina #palpalis is partial due to sequence gap in the assembly. #VBannotation
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