Moderator: Alex Reynolds
Alex Reynolds ♦ 29k
- Reputation:
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- Location:
- Seattle, WA USA
- Website:
- http://bitsumma.com/
- Twitter:
- AlexReynolds
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 hours ago
- Joined:
- 9 years, 11 months ago
- Email:
- a************@gmail.com
One of the developers behind the fast BEDOPS suite, whose pug Zac is the bestest pug in the world.
Posts by Alex Reynolds
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... If you need items presented as found in their original order:
$ awk '{ arr[$1] = arr[$1]"|"$0; } END{ for (k in arr) { s=arr[k]; n=split(s,a,"|"); for (i=2;i<=n;i++) { print a[i]; } print ""; } }' entries.txt
A 1 2 3 4 5 6
A 11 232 4 6 7 8
A 0 0 0 0 0 0
B 2 4 54 34 3 1 ...
written 3 hours ago by
Alex Reynolds ♦ 29k
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... Use `re` to find the start index positions of all instances of your string-of-interest (here, your start codon, or whatever).
$ python
>>> import re
>>> [m.start() for m in re.finditer('ATG', 'ATGCGATCGATCGATCGATCGCGCGCGCAGCTA')]
[0]
Replace with `ATGCGATCGATCGAT ...
written 6 hours ago by
Alex Reynolds ♦ 29k
3
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... Read up on ggplot, log-linear and log-log plots, and regression. ...
written 7 days ago by
Alex Reynolds ♦ 29k
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Answer:
A: Get SVG image of motif
... You could perhaps use Inkscape to import EPS and export SVG: https://inkscape.org/learn/faq/#what-formats-can-inkscape-importexport ...
written 16 days ago by
Alex Reynolds ♦ 29k
1
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4
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Answer:
A: Python FASTA scripting
... One approach I'd suggest uses standard input. This makes it very easy to test out different inputs:
#!/usr/bin/env python
import sys
import re
import os
import errno
sequence = ""
for line in sys.stdin:
line = line.rstrip()
if line.startswith('>' ...
written 19 days ago by
Alex Reynolds ♦ 29k
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Comment:
C: Python FASTA scripting
... Counterpoint: Biopython is slow, and learning to parse files with Python is an invaluable skill. It's a decent exercise for a beginning bioinformatician or someone learning Python. ...
written 19 days ago by
Alex Reynolds ♦ 29k
0
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... But without TF models from JASPAR or other sources, this is kind of a useless answer. Hopefully the OP can get in touch with some plant-specific TF specialists who can help him or her get the TF models needed to do this (on whatever scale). ...
written 19 days ago by
Alex Reynolds ♦ 29k
0
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... Could you review approaches here: http://planttfdb.cbi.pku.edu.cn/index.php?sp=Vun and here: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4306-1 for TF discovery? You might even contact authors for advice and code, to set up a collaboration to run things for your particular spec ...
written 19 days ago by
Alex Reynolds ♦ 29k
0
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1
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... Depends on your experiment, I guess. A reference genome rarely changes, but targets could easily do so. You only have to scan a reference genome once to build a "database" of binding sites. If your targets change, all you have to do is scan with `bedops` etc. against the reference binding sites, whi ...
written 19 days ago by
Alex Reynolds ♦ 29k
4
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1
answer
111
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1
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... You could run FIMO on your entire genome for TFs (transcription factors; DNA-binding proteins) of interest, which gives you binding sites: genomic intervals where those TFs bind. Here's a post where I wrote up step-by-step instructions:
https://bioinformatics.stackexchange.com/a/2491/776
Once you ...
written 19 days ago by
Alex Reynolds ♦ 29k
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