Moderator: Joe

gravatar for Joe
Joe18k
Reputation:
17,700
Status:
Trusted
Location:
United Kingdom
Website:
http://www2.warwick.ac...
Twitter:
JRJHealey
Last seen:
9 hours ago
Joined:
5 years, 1 month ago
Email:
j*********@gmail.com

Recently finished my PhD, so now I pretend to know what I’m talking about on Bioinformatics forums...

Currently a Research Fellow at the University of Warwick Medical School, and the CEO and Founder of biotech startup www.nanosyrinx.com

Posts by Joe

<prev • 3,118 results • page 1 of 312 • next >
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Comment: C: Biopython not installed correctly error when trying to call python script from R
... What happens if you try to invoke a dummy python command (so, not Biopython)? e.g. have `R` call a script which just prints out some version numbers or writes a dummy file. ...
written 17 hours ago by Joe18k
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Comment: C: Reading frames in python
... I think you may be overthinking/complicating the task, but it appears this is an assignment so I'm afraid we can't give fully functional code ;) You need to approach the problem in logical steps, which will broadly look like: Iterate over a string, capturing 3 characters at once, with an offset. ...
written 18 hours ago by Joe18k
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Comment: C: Protein/peptide characterization/properties tools
... I don't think many of these properties can be easily determined *in silico*, but you could start with `InterProScan`. You may need to break some of these categories down, for instance fold prediction could be anything from predicting secondary structure from a sequence, to full-on molecular dynamic ...
written 7 days ago by Joe18k
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Comment: C: MultiGeneBlast gui vs command prompt
... Can you post the directory structure and the exact command you're using on the commandline? ...
written 9 days ago by Joe18k
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Comment: C: Having some regex problems capturing strings with special chars. Could use some
... Is this a bioinformatics question? ...
written 11 days ago by Joe18k
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Comment: C: Time steps in node perturbation analysis
... It depends what the exact question is that you're asking? If the question is "how does expression of gene x differ at t=150, from t=0 then you just describe the state change. If the question asks you how the system has evolved in this time period then you will want to look at the shape of the curv ...
written 11 days ago by Joe18k
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Comment: C: Time steps in node perturbation analysis
... Is this a homework question? If you perturb a system, what does your intuition tell you about why you might want to observe this over an extended time period? There is no such thing as a perturbation fixed in time, a perturbation is only a perturbation relative to some observed behaviour of a syste ...
written 12 days ago by Joe18k
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Comment: C: BLAST search with multile fasta sequences and with a single output
... There is no way to get a 1-to-1 correlation from BLAST in one step. It will return you all the HSPs that fit your criteria for every sequence you give it. You will have to post-process the BLAST output file to obtain this. ...
written 12 days ago by Joe18k
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Answer: A: Replace FASTA file headers
... You can turn your substitutions file into a list of `sed` commands and run that on the file. Assuming your subs file is separated by spaces: Run: `sed -i -e 's|^|s\/|g' -e 's| \+|\/|g' -e 's|$|\/g|g' subs.txt` on the file containing the substitutions, which gives: s/>A_1/>B_1/g s/&g ...
written 13 days ago by Joe18k
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Comment: C: Basic Python problem on .pdb reading
... I'm not sure what you mean in (1), making an extensible list as a variable is the same as a regular list (`var = []` or `var = list()`). You can add and remove from lists using `list.append(item)` to add, and `list.pop(item)` or `list.remove(item)` to remove, depending on what you want to achieve ex ...
written 13 days ago by Joe18k

Latest awards to Joe

Appreciated 22 hours ago, created a post with more than 5 votes. For A: what are the big questions in bioinformatics field nowadays
Popular Question 7 days ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Scholar 16 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Things you wish you knew when entering the bioinformatics field
Scholar 4 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: what are the big questions in bioinformatics field nowadays
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Scholar 6 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 6 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: Run a Python program in Ubuntu
Scholar 9 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
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
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: Run a Python program in Ubuntu
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Scholar 11 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 12 weeks ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Run a Python program in Ubuntu
Scholar 3 months ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence

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