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The process of attaching contextual information to a biomolecular (DNA, RNA, or protein) sequence, such as the location of genes, promoters, or repeats in genomic DNA, or the function of a protein.

5
votes
The GFF3 file format specification doesn't care where annotations are described in the file, although it can make some things easier if the annotations are ordered by the start position: 1 T1 gene …
answered Jan 4 '18 by gringer
4
votes
I'm not too familiar with annotation pipelines, but based on a couple of Twitter posts it looks like Prokka might be a reasonable start. … Torsten Seeman (lead developer of Prokka) has done a post about alternative annotation pipelines: http://thegenomefactory.blogspot.co.nz/2013/03/bacterial-genome-annotation-systems.html …
answered Sep 18 '17 by gringer
2
votes
The response from NCBI suggests that there is a problem with either the sequence or annotation (e.g. nad5 extends into an annotated tRNA sequence). … Should we edit the annotation ourselves or there is a software that does it itself? If there is an error in the annotation through automated methods, you should fix it manually. …
answered Jul 3 '21 by gringer
0
votes
Answer from @devon-ryan, converted from comment: Try a UCSC gene ID instead. For those genes they'd be: uc001zni.3 (INO80), uc002vaz.4 (INO80D), uc004eup.4 or uc004eun.4 (SMARCA1) and uc001coj.2, uc01 …
answered Jul 4 '21 by gringer
1
vote
With the prompting from @Devon_Ryan's answer, I came up with a solution that worked well for me. I downloaded the mm10 RefSeq gene locations from UCSC [Fields: chrom, txStart, txEnd, name2], and sorte …
answered Jan 16 '18 by gringer
0
votes
As I mentioned in my answers to similar questions, there are a lot of cells with very high mitochondrial gene content. It would be a good idea to work out why that is before doing any more downstream …
answered Aug 11 '21 by gringer