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Why does a transcript sequence assembled by Trinity.fasta have many stop codons in the middle?
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#### Summary:
The complete nucleotide sequence retrieved from NCBI is written to the output, including any terminal stop codons.
These sequences often cannot be used for backthreading onto aligned p…
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Given a user-specified set of mutation(s), what is the reference codon and alternative codon(s) for each mutation?
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Refactor YAL5-single-codons.R and YAL5-codon-pairs.R to separate concerns within each script [Edward will provide requirements], comment using Roxygen2-style comments, add `testthat.R` compliant tests…
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Hi,
- I have noticed that when run on protein mode, BRAKER v3.0.3 will often have two identical transcripts for many genes. One created by AUGUSTUS, and one created by Genemark.hmm3.
- The only…
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The Protein Translation exercise deviates from the upstream canonical data by including additional proteins not listed in the instructions. Generally, that's fine, but in this circumstance, students w…
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- [x] Download `Complete Genome` from RefSeq
- [ ] Estimate codon usage bias: `CUB`
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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…
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KP.4+C10969T, A26579G,C23277T(S:T572I)+G174T+G22865T(S:A435S)
2 of the recent French seqs have their Orf10 start codon destroyed.
GISAID query: G22865T,C23277T,G174T
No. of seqs: 7(Canada 1 UK …
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It is my understanding that OrfM outputs continuous stretches of codons without a stop codon in the middle, but I am getting output with embedded stop codons, or what I believe are stop codons. I trie…