User: jrj.healey

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jrj.healey3.8k
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http://www2.warwick.ac...
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JRJHealey
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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 • 817 results • page 1 of 82 • next >
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Answer: A: Are there any working GNU parallel or similar Shell code examples on how to run
... Can you be more specific? What kind of files/what file structure? The format for `parallel` is pretty much the same for whatever you want to do: parallel 'mycommand {} {.}.ext' ::: inputfile(s)` The command is simply whatever you would normally invoke the program by. Here's a real example of ...
written 2 days ago by jrj.healey3.8k
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Comment: C: Add new sequence to clustalw2 alignment
... https://www.biostars.org/p/12066/ ...
written 2 days ago by jrj.healey3.8k
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Comment: C: Add new sequence to clustalw2 alignment
... Have you ensured you’re running a local alignment and not a global one? ...
written 2 days ago by jrj.healey3.8k
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Comment: C: How to derive phylo tree from two genes
... Theoretically yes, but the 'best' tree, may have polytomies, and you wont know that unless you look at the bootstraps. A tree with no bootstraps at all is pretty much meaningless. ...
written 4 days ago by jrj.healey3.8k
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Comment: C: How to derive phylo tree from two genes
... If you follow the RAxML documentation, there should be an output file called 'bestTree" or something to that effect. I would try for at least 300 bootstraps if you can manage it on your machine. There is a second step in the process to add the bootstraps on to the tree nodes from the bootstrap tree ...
written 4 days ago by jrj.healey3.8k
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Comment: C: How to derive phylo tree from two genes
... You can compute a species/consensus tree with the program ASTRAL-II, after generating gene trees with a tool of choice (I'd suggest IQ-Tree or similar). Its not going to be much of a consensus from just 2 different genes though, and 9 representatives may not produce the most robust trees. You coul ...
written 4 days ago by jrj.healey3.8k
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Comment: C: Passing multiple fasta files to local blast
... You could use the `multiprocessing` python module. Alternatively, use `subprocess` to pass `blast` commands to `GNU Parallel` at the commandline. How you batch up the files before invoking either of these would be entirely up to you in the python script. ...
written 4 days ago by jrj.healey3.8k
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Comment: C: make fasta sequence which is multiple of three
... I stand corrected on the pairwise in that case (I've never done it myself), but this is absolutely the workflow, so we all agree there! I'm curious though, if you're just using pairwise sequences, how can you decide which sequence is 'right' relative to the other? You'd have no other information ab ...
written 4 days ago by jrj.healey3.8k
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Comment: C: Annotating and predicting the genomic region of a sequenced phage
... Just take your contigs and run them through some annotation software. Prokka would probably do it. You’re likely seeing bacterial sequences because this phage is seen as a prophage in those bacterial genomes. ...
written 4 days ago by jrj.healey3.8k
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Comment: C: Genome Assembly at low coverage?
... I'd just assemble it and see what you get. If you assembly stats look reasonable (decent N50s etc), then I would probably, cautiously, continue. it depends what exactly you intend to do with this data. Even with a very good 8X assembly you probably won't be able to call SNPs etc. ...
written 5 days ago by jrj.healey3.8k

Latest awards to jrj.healey

Scholar 5 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 6 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 6 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
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
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
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
Scholar 10 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 10 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
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
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
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: fasta seq header
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
Scholar 4 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
Scholar 7 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 7 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
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
Scholar 7 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
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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