User: Anima Mundi
Anima Mundi • 2.4k
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Posts by Anima Mundi
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... Hello, in your shoes I probably would:
a) [retrieve all NCBI sequences for your *taxon*][1] in GenBank format
b) search for each gene description in your GenBank database (e.g. in the "Official Full Name" field)
c) fetch the corresponding gene symbol (i.e. in the "Official Symbol" field)
Hope th ...
written 6 weeks ago by
Anima Mundi • 2.4k
1
vote
4
answers
189
views
4
answers
... A Python 2.7 solution:
import sys
header = ''
seq = ''
j = 0
for line in open(sys.argv[1]):
j += 1
n = 0
for line in open(sys.argv[1]):
n += 1
if line[0] == '>':
print seq
seq = ''
for char in ...
written 8 weeks ago by
Anima Mundi • 2.4k
0
votes
3
answers
3.6k
views
3
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... Hi jleandroj,
When asked to enter the subject, you should copy-paste the genome sequence from its FASTA (or whatever sequence you want to parse for occurrences of the first one). Please just note that, as it is, the script is case-sensitive and does not allow newlines. Hope this helps. ...
written 10 weeks ago by
Anima Mundi • 2.4k
0
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1
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213
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1
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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 5 months ago by
Anima Mundi • 2.4k
0
votes
1
answer
213
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1
answers
... 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 5 months ago by
Anima Mundi • 2.4k
0
votes
2
answers
367
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2
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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 6 months ago by
Anima Mundi • 2.4k
0
votes
1
answer
202
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1
answers
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 6 months ago by
Anima Mundi • 2.4k
1
vote
1
answer
202
views
1
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Comment:
C: Change nexus textlabels
... Well, this was meant to reply to an original question, now missing -.-'' ...
written 6 months ago by
Anima Mundi • 2.4k
0
votes
1
answer
202
views
1
answers
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 6 months ago by
Anima Mundi • 2.4k
2
votes
1
answer
295
views
1
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 6 months ago by
Anima Mundi • 2.4k
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