Moderator: Joe
Joe ♦ 18k
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- United Kingdom
- Website:
- http://www2.warwick.ac...
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- JRJHealey
- Last seen:
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- Joined:
- 5 years, 1 month ago
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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
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... 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
Joe ♦ 18k
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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
Joe ♦ 18k
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... 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
Joe ♦ 18k
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... Can you post the directory structure and the exact command you're using on the commandline? ...
written 9 days ago by
Joe ♦ 18k
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... Is this a bioinformatics question? ...
written 11 days ago by
Joe ♦ 18k
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... 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
Joe ♦ 18k
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... 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
Joe ♦ 18k
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... 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
Joe ♦ 18k
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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
Joe ♦ 18k
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... 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
Joe ♦ 18k
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