Moderator: jrj.healey
jrj.healey ♦ 12k
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- United Kingdom
- Website:
- http://www2.warwick.ac...
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- JRJHealey
- Last seen:
- 7 hours ago
- Joined:
- 3 years, 9 months ago
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Recently finished my PhD, so now I pretend to know what I’m talking about on Bioinformatics forums...
Posts by jrj.healey
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... I would argue that unless you want to make your research career focus a specific organism, the fungal aspect isn’t really relevant.
Someone who can code, knows the general concepts of genome assembly, or transcriptomics or what have you, has the skill set to transfer to any organism. ...
written 12 hours ago by
jrj.healey ♦ 12k
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Comment:
C: ORF reading in Python
... At a quick glance you may need to show us more of the script, where these functions are actually called. Based on your output I’d guess that your loop over your file is incorrect, rather than your ORF finding. ...
written 15 hours ago by
jrj.healey ♦ 12k
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C: BLAST using Biopython
... Great. I’ve moved the comment to an answer, so if you’re happy with the resolution to the thread, please go ahead and toggle the Tick to accept the answer as a solution. ...
written 2 days ago by
jrj.healey ♦ 12k
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... There’s a commandline version of `Espript` IIRC. That would probably work.
I also like the TeX package `texshade` for rendering MSAs, if you’re prepared to get your hands dirty with TeX.
I’ll post an example when I’m at a proper computer. ...
written 2 days ago by
jrj.healey ♦ 12k
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Comment:
C: root to node distance
... By time, do you mean actual time - like dates? Or do you just want to know the distance?
These are 2 very different questions. ...
written 2 days ago by
jrj.healey ♦ 12k
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... At a very quick glance here: https://biopython.readthedocs.io/en/latest/Tutorial/chapter_graphics.html#annotated-chromosomes
I think you will basically want to create custom features which correspond to the length of span of each chunk of the ancestral parts, essentially treating them like one real ...
written 3 days ago by
jrj.healey ♦ 12k
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... Indexing is almost certainly the right way to do this. Even with `biopython` which will typically be slower, its likely do-able using `SeqIO`'s `index()` method ( https://biopython.org/wiki/SeqIO ):
from Bio import SeqIO
index = SeqIO.index('bigfasta.fa', 'fasta')
print(index['myf ...
written 3 days ago by
jrj.healey ♦ 12k
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... Perhaps take a look at PAML? I think it has a fairly extensive (but probably complicated) dNdS analysis suite. ...
written 5 days ago by
jrj.healey ♦ 12k
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... The best solution, I feel, would simply be to run this over all the 'jumbled' data, and ensure you have everything in the correct orientation before proceeding. Once you have done so, you can concatenate them or whatever, and proceed to make the tree.
If the sequences are in the correct orientation ...
written 6 days ago by
jrj.healey ♦ 12k
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... Sorry, I'm not familiar with AMPHORA, so I'm not sure what it does.
Are the sequences which are reversed on their own in a single file, or mixed in with the sequences which are 'forward'?
Please post a small representative example of the fasta file with the headers and reversed sequences. ...
written 6 days ago by
jrj.healey ♦ 12k
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For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
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For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
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