User: jrj.healey
jrj.healey • 1.9k
- Reputation:
- 1,940
- Status:
- Trusted
- Location:
- United Kingdom
- Website:
- http://www2.warwick.ac...
- Twitter:
- JRJHealey
- Last seen:
- an hour ago
- Joined:
- 1 year, 10 months ago
- Email:
- j*********@gmail.com
PhD Student at the Molecular Organisation and Assembly in Cells Doctoral Training Centre, University of Warwick.
PhD is lab based primarily, utilising synthetic biology for drug delivery applications, but something of an amateur enthusiast when it comes to bioinformatics/programming. Trying to absorb as much as I can.
Decent amount of experience with molecular simulation, genomics (including assembly, QC, annotation, comparative genomics), transcriptomics, proteomics, phylogenetics etc.
Posts by jrj.healey
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... Can't think of anything significant which would make one better than the other. Accessibility usually gives the edge to cloud based set ups (not everyone has the luxury of a private server or cluster). If you use cloud based VMs, you have the bonus of the server being 'all yours' for a while, so you ...
written 10 hours ago by
jrj.healey • 1.9k
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... Unless the fasta's are linearised, as in the above comment, then no not really. I might be *possible*, but would be ugly and clunky I'm sure. ...
written 2 days ago by
jrj.healey • 1.9k
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... Agreed, BioPython is totally the way to go for this ...
written 3 days ago by
jrj.healey • 1.9k
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... You'd be better off using HMM profiles or similar for an alignment. If you're adamant about doing it your way, you can use Biopython to get a Posititon-Specific-Score-Matrix which will give you proportions of each residue at each position, which is basically the information that's in a MeMe logo. ...
written 3 days ago by
jrj.healey • 1.9k
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... You just want the sequences of all the transcripts first? ...
written 4 days ago by
jrj.healey • 1.9k
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105
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... You want to use the motif for tree construction? Why/How? ...
written 4 days ago by
jrj.healey • 1.9k
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Comment:
C: Entrez.esearch url bug
... Right you are. Unbeknownst to me, the requirements.txt was using biopython 1.65. Moving to 1.70 seems to have fixed it. ...
written 4 days ago by
jrj.healey • 1.9k
0
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... Yeah I'm certain your output file specification is probably breaking something. Try something like:
for file in snp_table_files/* ; do
perl ./script.pl "$file" population.txt ./outfiles/"${file%.*}".txt.out
done ...
written 5 days ago by
jrj.healey • 1.9k
0
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1
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162
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... What is the error you get? Empty files?
When you say in parallel, do you mean in parallel? Because your code runs them sequentially. ...
written 5 days ago by
jrj.healey • 1.9k
2
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1
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122
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... Currently troubleshooting a Twitter bot that broke down, and it seems to be failing to retrieve from the Entrez API whereas it was working until about 2 weeks ago.
Has something changed in the Entrez API or is this a biopython issue?
It seems to come down to this, though there may be other issues ...
written 5 days ago by
jrj.healey • 1.9k
• updated
4 days ago by
Istvan Albert ♦♦ 73k
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For A: Script/Application to create a genbank format sub-sequence
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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: Script/Application to create a genbank format sub-sequence
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11 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
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11 weeks ago,
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For A: Script/Application to create a genbank format sub-sequence
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11 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
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For A: Replace Sequence IDs in many text files (newick format) - Change script
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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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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
Scholar
3 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Teacher
4 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
4 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Appreciated
4 months ago,
created a post with more than 5 votes.
For A: Replace Sequence IDs in many text files (newick format) - Change script
Scholar
4 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Teacher
4 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
4 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
Scholar
4 months ago,
created an answer that has been accepted.
For A: Script/Application to create a genbank format sub-sequence
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