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I was working on a 19-nt tRF which sequenced as follows:
`GACCGCAUAGCGCAGUGGA`
I tried the built-in Arabidopsis database with the web server and a self-built rice database (IRGSP1.0) on a local m…
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Hi Adam,
if my method of getting the sequences of the identified fragments from the fasta file was correct, there might be something off in my application of the pipeline. I was not able to find an…
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**Current term details**
```
Term name - assembly quality
Term ID - [MIXS:0000056]
Structured comment name - assembly_qual
Definition - The assembly quality category is based on sets of criteria…
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This is a proposal to improve feature profiling for the identification of tRNAs from tRNA-seq libraries and to benchmark the profiling algorithm with high-scoring tRNA gene predictions from a database…
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hi adam,
i finally had time to look at the results, found another bug (will make separate issue), but got it to work in the end. i am in the QC_alignment.Rmd, and i was wondering what the BED file …
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Hello. I installed gffread 0.12.1 through anaconda and used to convert a GFF3 file into GTF format.
The file I used is the gff3 annotation file from Araport11:
[https://www.arabidopsis.org/download_…
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Most of the tRNAs have no products
http://japonicusdb.kmr.nz/results/from/id/3d8939a6-271b-49c3-84fd-c348f127c5ed
Are these missing from the gff file? If so I suggest for now that we just stic…
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### Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above.
rRNA and tRNA are thought to be difficult to be assembled from…
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## Short description of the problem
The `--min-alignment-fraction` parameter of `anvi-dereplicate-genomes` is not working as expected.
## anvi'o version
I'm using the master version as of thi…
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Beginning with sequence-based searches of the literature via PaperBLAST and using the sequences acquired from PomBase, UniProtKB