-
Would be cool to allow users to input custom codon usage tables and/or draw from the database here https://dnahive.fda.gov/dna.cgi?cmd=cuts_main
-
Hi,
I am trying to repeat part of your work to generate diverse coding sequence, but I could not find the host codon usage table, such as CLIB_release.csv for the Y. lipolytica or files for the E. co…
-
## Short description of the problem
When running `anvi-get-codon-frequencies`, there is a TypeError in how pandas is used in `_make_gene_codon_frequency_table`.
## anvi'o version
```
Anvi'o …
-
I work on Gram-positive actinobacteria, which can frequently encoded alternative starts. I've noticed some genes are annotated with a wrong start (frequently too long to comply with an ATG start inste…
-
Hi Fabio,
First, thanks for developing this fantastic tools. I have been use to this tool for analysis several datasets and get amazing result.
However, when I am trying to use RiboWaltz to ana…
-
- [x] Download `Complete Genome` from RefSeq
- [ ] Estimate codon usage bias: `CUB`
-
Hi,
It could be interesting to extract the number of TAG, TAA, TGA used as STOP codon from Prodigal CDS prediction.
@ylana Do you think you can do that? You can take inspiration from the script `s…
-
Hello,
I have a request that should enhance the utility of DNA Chisel for codon optimization.
When selecting Codon Usage Tables for species [not included](https://github.com/Edinburgh-Genome-Fou…
-
Hi Anamaria,
I would like to suggest you to incorporate also the work on codon usage bias and its linkage to growth rate in genomic/metagenomic data as introduced in Vieira-Silva & Rocha (https://jou…
-
Hi,
I got an error message with the term 'sort' that is used three times in the script. It appears the term is deprecated and now need to use either sort_values or sort_index. Which should be used i…
pkvaz updated
6 years ago