User: Anima Mundi
Anima Mundi • 2.4k
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Posts by Anima Mundi
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... Dears,
I have an mRNA sequence stored as a local file. I retrieved it from GenBank in late 2016 (ID: XM_014915109.1). I just found out that the sequence now appears to be different, but apparently nothing in its GenBank page notifies there were changes after 2016. While it is of course possible tha ...
written 9 months ago by
Anima Mundi • 2.4k
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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 11 months ago by
Anima Mundi • 2.4k
1
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4
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... 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 11 months ago by
Anima Mundi • 2.4k
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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 11 months ago by
Anima Mundi • 2.4k
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475
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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 15 months ago by
Anima Mundi • 2.4k
0
votes
1
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475
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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 15 months ago by
Anima Mundi • 2.4k
0
votes
2
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709
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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 15 months ago by
Anima Mundi • 2.4k
0
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1
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379
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1
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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 15 months ago by
Anima Mundi • 2.4k
1
vote
1
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379
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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 15 months ago by
Anima Mundi • 2.4k
0
votes
1
answer
379
views
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 15 months ago by
Anima Mundi • 2.4k
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