User: jrj.healey

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jrj.healey1.5k
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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 • 346 results • page 1 of 35 • next >
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Comment: C: Create genbank files by plasmid
... Can you make it clearer what you mean? What are the 'plasmid clusters'? If you need to split genbanks up from a multiple, to individual ones, you can have a look at my code in this answer: https://www.biostars.org/p/230441/#230459 ...
written 3 days ago by jrj.healey1.5k
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Comment: C: MToolBox.sh: line 173: check_files.py: command not found
... Even if you are in the folder where the file exists, if the folder isn't in the PATH, you would have to call the script/program with a filepath, e.g. `$ ./setup.sh` or it's full path, `$ setup.sh` wouldn't be sufficient. ...
written 3 days ago by jrj.healey1.5k
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Comment: C: Grep Position List
... On the theme of filtering column-oriented files, if you are prepared to code stuff up yourself, consider `awk` within the shell, or modules like `csv` within python etc. ...
written 5 days ago by jrj.healey1.5k
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Comment: C: Reference guided assembly of contigs
... Just install SOAP/Velvet/MIRA or any other number of assemblers that have a reference guided option. You can often install (well written) software in your local or home directory on a server. ...
written 7 days ago by jrj.healey1.5k
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Circular alignment comparisons
... Does anyone have a guide on how to create circular MSA comparisons with (for example) Circos? I've tried AliTV, which creates the relevant alignments with `lastz` and can be displayed either in linear or circular format, like so: ![enter image description here][1] [1]: https://i.imgur.com/1iPb ...
circos written 7 days ago by jrj.healey1.5k
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Comment: C: Software for Tree Visualization
... ETE3 is my absolute favourite commandline tool. the `--text` tree view is so neat to quickly glance at a tree without having to open an Xterm window ...
written 7 days ago by jrj.healey1.5k
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Comment: C: [BioPython] Parse blast tabular output
... Have you tried using `SearchIO` with the blast tabular output? It's pretty straighforward. e.g: blast_result = SearchIO.read(resultHandle, 'blast-tab') print(blast_result[0][0]) start = blast_result[0][0].hit_start end = blast_result[0][0].hit_end Also, you can treat the `outfmt 6` as just ...
written 7 days ago by jrj.healey1.5k
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Answer: A: Software for Tree Visualization
... As mentioned: - ggtree - FigTree (my favorite) - njplot - ETE3 - Dendroscope The list goes on... Also if you just google your post title pretty much, you'll get this: https://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software ...
written 8 days ago by jrj.healey1.5k
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Comment: C: Map fasta headers based on sequence match
... If the strings are exactly the same as you say, you can do it with simple string matching. ...
written 13 days ago by jrj.healey1.5k
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Comment: C: PCAs, how to interpret the scale of the axis
... Why would you expect that the scales would be the same? They're different variables accounting for a different amount of the variance in that data set. The magnitude of the variance itself between 2 variables isn't really comparable. ...
written 17 days ago by jrj.healey1.5k

Latest awards to jrj.healey

Scholar 17 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 21 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 21 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 22 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
Commentator 25 days ago, created a comment with at least 3 up-votes. For C: fasta seq header
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Replace Sequence IDs in many text files (newick format) - Change script
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
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
Guru 6 weeks ago, received more than 100 upvotes.
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Teacher 8 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 8 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 11 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Replace Sequence IDs in many text files (newick format) - Change script
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
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
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
Centurion 3 months ago, created 100 posts.

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