User: Anima Mundi
Anima Mundi • 2.3k
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Posts by Anima Mundi
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... Assuming you performed your PCR on cDNA, checking for amplicons from genome is merely a way to check for potential sources of genomic contamination. Doing this using your whole amplicon would just return genomic locations in which your full amplicon (or something thereof) is present, if any. For ins ...
written 2 days ago by
Anima Mundi • 2.3k
0
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1
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... Hello,
a rapid way to do that is to:
1) reverse-complement (RC) your right primer
2) build your subject database as a FASTA file (if needed)
3) go to [NCBI nucleotide BLAST][1]
4) paste your left primer, type a series of Ns right next to it, then paste your RC right primer
5) load your databas ...
written 2 days ago by
Anima Mundi • 2.3k
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Comment:
C: transition to bioinformatics
... Hi, just a quick comment.
> But I really want this, I really like it.
Just roll with it ;)
Nowadays there is a strong need for bioinformaticians, if you happen to have a strong interest for bioinformatics and you are fresh from a degree in biology then you are in luck, in my opinion. ...
written 13 days ago by
Anima Mundi • 2.3k
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Comment:
C: Change nexus textlabels
... Yep, indeed the script was simply meant to help you re-format your list IDs, as you originally requested. If you want to get some help then... you should help people to help you! For instance, in the original question at least you were pointing out to one example ID. That said, unfortunately I am no ...
written 27 days ago by
Anima Mundi • 2.3k
1
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1
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Comment:
C: Change nexus textlabels
... Well, this was meant to reply to an original question, now missing -.-'' ...
written 27 days ago by
Anima Mundi • 2.3k
0
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1
answer
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1
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Answer:
A: Change nexus textlabels
... Hi, if you want to try replacing headers, this should do the job (Python 2.7 script, takes the two list filenames as arguments):
import sys
listA = []
listB = []
for line in open(sys.argv[1]):
listA.append(line.replace('\n',''))
for line in open(sys.argv[2 ...
written 27 days ago by
Anima Mundi • 2.3k
2
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1
answer
154
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answers
... Hi, welcome.
To make your restriction map:
a) consider the coordinates of your gene irrespective of its sense strand, i.e. `chr11:355953-356144`
b) it is useful to expand its coordinates a bit both upstream and downstream (because you are interested in restriction sites surrounding it); say, we e ...
written 4 weeks ago by
Anima Mundi • 2.3k
0
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2
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237
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... I see, then I think you should be just fine with the MEME suite, what is your problem exactly? ...
written 12 weeks ago by
Anima Mundi • 2.3k
1
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... Hello, did you attempt to use MEME via command line or the web version of it? In the second case, I would just recommend switching to command line. ...
written 12 weeks ago by
Anima Mundi • 2.3k
0
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2
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505
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... Just for the fun of discussing: what I see is that a recurrent theme among "hard" scientists (i.e. those having a background in physical - as opposed to natural - sciences) is that biology can be approximated to a list of notions. I disagree with that view: while notions in biology are certainly imp ...
written 3 months ago by
Anima Mundi • 2.3k
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For A: Retrieving RNA sequence from corresponding genomic coordinates
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For How To Use Bedtools To Extract Promoters From A Mouse Bed File
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