User: jrj.healey

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jrj.healey3.4k
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United Kingdom
Website:
http://www2.warwick.ac...
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JRJHealey
Last seen:
2 hours ago
Joined:
2 years, 5 months ago
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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 • 712 results • page 1 of 72 • next >
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Comment: C: Difficult using Nanoplot
... Paging @ https://www.biostars.org/u/24526/ ...
written 16 hours ago by jrj.healey3.4k
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Comment: C: Submitting Pre-printed Articles
... Is the journal you had accepted open access? If not, the journal may own some or all of the copyright, so posting it online again could land you in trouble. Make sure you know their rules and regulations. ...
written 1 day ago by jrj.healey3.4k
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Answer: A: Finding novel domains in a group of proteins
... Its a computationally expensive approach, but you could try a mix of threading and ab initio structure prediction. Sequences diverge much more quickly than do structures, so you may be able to try a 'brute force' in silico protein-protein docking approach. You may simply not be able to 'see' this d ...
written 1 day ago by jrj.healey3.4k
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Comment: C: Creating a pathway with requirements
... Is this a bioinformatics exercise or a molecular biology exercise? ...
written 2 days ago by jrj.healey3.4k
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Answer: A: massive pairwise sequence alignment
... Something else you could do is use the CD-HIT suite to cluster the sequences to a particular stringency. I don’t know how it will handle that many sequences specifically, but it’s usually quite fast I think. ...
written 2 days ago by jrj.healey3.4k
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Comment: C: Retrieve sequences that generated a HMM profile
... `hmmemit` is your only option as far as I'm aware. It doesn't randomly emit a sequence, it produces the most likely sequence given the hidden states of the Markov Model profile (a kind of consensus sequence). ...
written 2 days ago by jrj.healey3.4k
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Comment: C: Can't find a pattern in heatmap, is it okay?
... Are you expecting to see one? Why? Heatmaps are just a visualisation tool, not really an analysis tool. Besides, there's a marked difference between your tumor and WT control as far as I can tell. YOu should probably do an ontology exploration to figure out the story behind your data. ...
written 2 days ago by jrj.healey3.4k
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Comment: C: Assembly of 454 raw data (in fastq)
... I thought (though I may well be wrong) that Velvet or SOAP was originally developed for 454 sequencing. ...
written 3 days ago by jrj.healey3.4k
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Comment: C: Multiple Sequence Alignment for very large data sets
... Assuming the logic/experiment is all sound - try a different tool. Ones that tend to be good for large scale: - progressiveMauve - LASTZ - Kalign ...
written 3 days ago by jrj.healey3.4k
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Comment: C: BioVM - a virtual machine for Bioinformatics
... Without wishing to sound too negative, what does this do that BioLinux doesn't already? ...
written 3 days ago by jrj.healey3.4k

Latest awards to jrj.healey

Popular Question 7 days ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Teacher 13 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 14 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 14 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 21 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
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
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
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Teacher 9 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 9 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 12 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 12 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
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 4 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Scholar 5 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 5 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 5 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 5 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 5 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 6 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Voter 7 months ago, voted more than 100 times.
Scholar 8 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence

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