Blake Sweeney

Detect possible protein coding sequences

2

There appears to be protein coding sequences in RNAcentral. For example: http://rnacentral.org/search?q=%22protein%22%20and%20not%20%22non-protein%22 http://rnacentral.org/search?q=hypothetical%20protein http://rnacentral.org/search?q=open%20reading%20frame Not all of the results from these searches produce things that are really protein coding. Some...

JSON download does not contain as many sequences as advertised

1

I downloaded search results in JSON from http://rnacentral.org/export/results?job=fdb8a27d-bf41-443a-ad51-64919244db8f, which states there are 12405 sequences. After downloading with safari, examining the file at the command line with jq gives 12367.

Downloading json files give a file that is gzipped twice

1

The file ends up having to be gzip -d twice if downloaded through safari. Steps: 1. Go to 'http://rnacentral.org/export/download-result?job=4e4dc29d-c53d-41a3-be5f-54908ec622f3' 2. Hit download 3. Try the following: ```sh ✔ bsweeney@bsweeney-ml ~/Downloads...

It would be useful to allow users to download results of a search in BED/GFF(3) format. We will have to do something to inform the users that they are only...

Review what the API and downloads provide

1

To look into the pombe issues I downloaded some JSON data. In it I didn't see a mention of the computed `rna_type`. I also didn't see it in API, eg...

@AntonPetrov found that some sequences are missing a mapping from the accession to the reference. He found the sequences with: ```sql select * from xref t1, rnc_reference_map t2 where t2.ACCESSION...

At PAG Tanya from TAIR suggested that we create shorter URS ids. She said that it is hard to write down an id when displayed in a talk. While we...

We now index the 'tax_string' of accessions. This lets us make the species sunburst clickable. So for example, when hovering over the 'Bacteria' ring in http://test.rnacentral.org/expert-database/gtrnadb I would like to...

They may not be ordered and named ideally. - [ ] Rename tools to something clearer (or remove it entirely) - [ ] Reorder tabs by usage

There are few things to do to a genome browser to make it more useful. - [x] Use names other than RNAcentral URS ids on the view. - [ ]...