Moderator: jrj.healey

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jrj.healey12k
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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

<prev • 2,252 results • page 1 of 226 • next >
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Comment: C: PhD: Research interest or better program?
... 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.healey12k
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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.healey12k
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Comment: 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.healey12k
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Answer: A: Is there a command line tool that can take an alignment fasta and input and outp
... 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.healey12k
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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.healey12k
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Comment: C: Biopython chromosome drawing with coloring
... 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.healey12k
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Answer: A: Fast way to extract specific sequences from large fasta
... 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.healey12k
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Comment: C: Calculate dNdS pvalue in a multiple sequence alignment
... 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.healey12k
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Answer: A: Why does phylogenetic tree topology changes, among nucleotide and amino acid seq
... 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.healey12k
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Comment: C: Why does phylogenetic tree topology changes, among nucleotide and amino acid seq
... 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.healey12k

Latest awards to jrj.healey

Scholar 5 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Appreciated 5 days ago, created a post with more than 5 votes. For Interesting/useful/beautiful bio sequence viz tools
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 10 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Commentator 17 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 25 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 4 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 5 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 5 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Commentator 7 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 8 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 3 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence

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