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Hi Ryan,
Great tool! I've been using it for a couple of side projects and seems to work great (python3 version). However, now I want to submit some human cytomegalovirus genomes (HCMV) and I found …
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Hey, I would like to use predict_GPU.py to identify lncRNAs from putative ncRNAs of a transcriptome (~100k putative ncRNAs, >300bp). I didn't understand how to generate a file like file_format_GPU for…
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We list the proteins present in a structure, but not the ncRNAs. For example, this structure has U2 snRNA. I presume these have RNACentral IDs , so we might be able to get these IDs too from a mappi…
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@bahler
https://www.pombase.org/term/PBO:0006231
Exmaples with an almost identical RNA on the opposite strand:
SPNCRNA.279
SPNCRNA.280
SPNCRNA.158
SPNCRNA.156
SPNCRNA.398
SPNCRNA.163
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Hi,
when running prokka 1.14.6 with --rfam 0 ncRNAs are found. With prokka 1.13 several were detected and running the cmscan code from the logfile separately also resulted in the detection of sever…
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When using RNAcentral IDs for human ncRNAs, the URS is displayed in Noctua/Alliance pathway view. Could this be replaced with the symbol?
e.g. http://noctua.geneontology.org/workbench/noctua-visual…
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Some of the merged ncRNAs will have expression data associated with the synonyms.
We could display this also, on the merged feature (it should be fairly similar, since they are the same feature).
Pr…
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- [ ] literature search for compensatory mutations in mouse and human for RRIs
- [ ] find RRIs for lncRNAs to test specific model for ncRNAs
- [ ] look at Benchmark data for examples
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### Aims/objectives.
The nomenclature for RNA types (table `rna_type`) is fixed *e.g.*
```mysql
+---------+-------------------+
| id | name |
+---------+-------------------+
…
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**long non-coding RNA**: I used definition from wikipedia: Long non-coding RNAs (long ncRNAs, lncRNA) are non-protein coding transcripts longer than 200 nucleotides.
Alternative term: lncRNA
Parent: …