murphyte

uORF name or definition change

1

We are looking at adding a regulatory_class for uORF or regulatory_uORF to the INSDC specifications, and are trying to sync up with SO. SO term: uORF (SO:0002027) The current term...

edits for circular_ncRNA SO:0002291

1

Hi SO, There are a few tweaks needed for the entry for circular_ncRNA, originally discussed on #490. http://www.sequenceontology.org/browser/current_svn/term/SO:0002291 1. For synonyms, convert "circRNA" to "INSDC_qualifier:circRNA" and add "INSDC_feature:ncRNA". Compare to...

clarification on "match" terms

2

Hi SO -- I'm looking for clarification on a couple of the "match" SO terms: 1. For "translated_nucleotide_match" (SO:0000181), is that for alignments with nucleotide in column 1, and protein...

request for new terms related to bonds

5

Hi SO, We're trying to improve our mappings of INSDC to SO terms, and I'd like to request a few additions and revisions related to protein bonds. These aren't exactly...

instability in repeat names/class/family

2

We're seeing instability in repeat names and class/family for otherwise identical repeats. Here's a partial diff of two runs on the same sequence (GenBank GL456393.1, from mouse), both with: RepeatMasker...