User: jrj.healey

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jrj.healey2.9k
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United Kingdom
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http://www2.warwick.ac...
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JRJHealey
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an hour ago
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2 years, 2 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 • 597 results • page 1 of 60 • next >
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Answer: A: Mutation Rates calculation
... You can’t explicitly calculate **Mutation rate** as it’s impossible to observe all mutations. You can compare multiple sequence and extrapolate the **substitution rate**, but this is always lower than the real mutation rate. (If this doesn’t make intuitive sense, consider the example where the tran ...
written 1 day ago by jrj.healey2.9k
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Answer: A: Extract reads from fasta file (specific read_names)and make a new fasta file
... Here's the script I created to retrieve fasta's by key. https://github.com/jrjhealey/bioinfo-tools/blob/master/fastafetcher.py It assumes your list of keys is a simple line separated column of strings. key1 key2 key3 Then just invoke: python fastafetcher.py -f myseqs.fasta -k my ...
written 2 days ago by jrj.healey2.9k
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Comment: C: Doctor looking fertility for a collaborator for text mining on pubmed
... How extensive do you want this text mining to be? If you're just looking for keywords, pubmed/NCBI allows you to save searches (with potentially quite complicated syntax such as `"Smith, J[author] AND sequencing"`) and have the searches repeated weekly and delivered straight to your email inbox. ...
written 2 days ago by jrj.healey2.9k
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Comment: C: Doctor looking fertility for a collaborator for text mining on pubmed
... Not sure if 'terrific' is meant to mean 'causing terror' or someone is just a really big fan of endometriosis. ![enter image description here][1] [1]: http://i0.kym-cdn.com/photos/images/newsfeed/000/131/399/fry.PNG?1307468855 ...
written 2 days ago by jrj.healey2.9k
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Answer: A: Fasta header trimming for multiple delimiters
... Pure bash alternative: #!/bin/bash # usage: # $ bash extract_header_field.sh seqs.fasta while read line ; do if [ ${line:0:1} == ">" ] ; then IFS='|' read -a header <<< "$line" else seq="$line" ...
written 3 days ago by jrj.healey2.9k
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Comment: C: How to produce a consensus genome
... If you mean you just want to build a single genome but from 2 sets of input reads, you can simply `cat` The R1 files together, and then do the same for the R2, and run your assembler on the “uber” reads. ...
written 3 days ago by jrj.healey2.9k
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Comment: C: what is the problem with using clustal to do pairwise alignment?
... Were they using the same mismatch/gap/extend penalties? ...
written 3 days ago by jrj.healey2.9k
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Comment: C: Creating PDB file for peptide bonds
... I'm guessing now, but tools like JMol, Mercury, and ChemDraw might do this? ...
written 4 days ago by jrj.healey2.9k
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Answer: A: Creating PDB file for peptide bonds
... This is a somewhat hacky way to do it, but I’ve used ITASSER to generate structures for polypeptides as short as 10 AAs in the past. You just write the fasta by hand, and submit it to be ‘simulated’. This is massively overkill for sure, but shouldn’t take long at all with such a short chain. ...
written 4 days ago by jrj.healey2.9k
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Comment: C: what is the problem with using clustal to do pairwise alignment?
... Did you eye-ball the alignment that you got? I also (naively perhaps) would have expected Clustal to be fine with pairwise too. You can check the alignment by eye though to see if it does look screwy. ...
written 4 days ago by jrj.healey2.9k

Latest awards to jrj.healey

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
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Scholar 9 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 9 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
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 12 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 12 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 3 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Voter 4 months ago, voted more than 100 times.
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
Teacher 6 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
Teacher 6 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
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Appreciated 7 months ago, created a post with more than 5 votes. For A: Replace Sequence IDs in many text files (newick format) - Change script
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Teacher 7 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 7 months ago, received more than 100 upvotes.
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
Teacher 7 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

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