User: jrj.healey

gravatar for jrj.healey
jrj.healey1.9k
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

<prev • 421 results • page 1 of 43 • next >
0
votes
1
answer
120
views
1
answers
Comment: C: Cloud Computer Cluster VS Local Compute Cluster for RNAseq analysis
... 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.healey1.9k
1
vote
3
answers
218
views
3
answers
Comment: C: fasta files: keep only lines containing certain characters + the respective sequ
... 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.healey1.9k
0
votes
3
answers
218
views
3
answers
Comment: C: fasta files: keep only lines containing certain characters + the respective sequ
... Agreed, BioPython is totally the way to go for this ...
written 3 days ago by jrj.healey1.9k
1
vote
0
answers
105
views
0
answers
Comment: C: Can we use MeMe motif output result and prepare tree from motif
... 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.healey1.9k
0
votes
0
answers
87
views
0
answers
Comment: C: Determining the correct reading frames for transcripts for dn/ds calculation
... You just want the sequences of all the transcripts first? ...
written 4 days ago by jrj.healey1.9k
2
votes
0
answers
105
views
0
answers
Comment: C: Can we use MeMe motif output result and prepare tree from motif
... You want to use the motif for tree construction? Why/How? ...
written 4 days ago by jrj.healey1.9k
0
votes
1
answer
122
views
1
answers
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.healey1.9k
0
votes
1
answer
162
views
1
answers
Comment: C: running a perl script multiple times; input and output files are required
... 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.healey1.9k
0
votes
1
answer
162
views
1
answers
Comment: C: running a perl script in parallel multiple times; input and output files are req
... 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.healey1.9k
2
votes
1
answer
122
views
1
answer
Entrez.esearch url bug
... 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 ...
biopython written 5 days ago by jrj.healey1.9k • updated 4 days ago by Istvan Albert ♦♦ 73k

Latest awards to jrj.healey

Commentator 20 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
Commentator 21 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
Voter 21 days ago, voted more than 100 times.
Scholar 5 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
Scholar 10 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 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
Scholar 11 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 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
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Appreciated 3 months ago, created a post with more than 5 votes. For A: Replace Sequence IDs in many text files (newick format) - Change script
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
Guru 3 months ago, received more than 100 upvotes.
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
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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 952 users visited in the last hour