User: natasha.sernova
natasha.sernova • 3.4k
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Posts by natasha.sernova
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... As far as I have understood, a person who asked a question
was going to get a position of some fragment in a larger sequence.
But that particular fragment may differ a little bit from a real plasmid
sequence. The matrix I suggested a few days ago is an ancient approach,
but it would help. The a ...
written 2 hours ago by
natasha.sernova • 3.4k
0
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... I 've seen this post that should help to find identical residues.
https://www.biostars.org/p/318684/#319376
I hope it may help you. ...
written 3 hours ago by
natasha.sernova • 3.4k
0
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... The sequence you've provided is not a whole plasmid sequence, right?
It looks like some gene upstream. In this or similar cases you have to find
orthologous gene upstreams (the same gene from close species), find out, how
your site looks like there, then make a PWM (position weight matrix) - ...
written 1 day ago by
natasha.sernova • 3.4k
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Comment:
C: CpG islands prediction
... See this post from 'Biostars': https://www.biostars.org/p/79046/
https://www.biostars.org/p/57380/
A few other articles:
1)https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2883304/
Biostatistics. 2010 Jul; 11(3): 499–514.
Redefining CpG islands using hidden Markov models
Hao Wu, Brian Caffo, Harris A ...
written 3 days ago by
natasha.sernova • 3.4k
0
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1
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119
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... It seems you need a simple python script like this one below:
"""
string: AGTGTTAAGAAGTCCGT
and the recognition site is something like:
AAGAAG
"""
def posit_in_seq(string,site):
len_site = len(site)
if site in string:
for i in range (0, l ...
written 3 days ago by
natasha.sernova • 3.4k
1
vote
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84
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Comment:
C: scRNA-seq non-technical article
... I am not sure if it's possible to make the topic really popular.
These articles below look clear and understandable.
A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications
Ashraful Haque, Jessica Engel, Sarah A. Teichmann and Tapio Lönnberg
Genome Medic ...
written 3 days ago by
natasha.sernova • 3.4k
2
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... There are a lot of posts in "Biostars" about it.
Start with this one:
https://www.biostars.org/p/325071/
Then look at the right panel of the post above, you will see a lot of similar posts.
If it's not enough, go to the upper left corner, select LATEST and type your question to
the empty string ...
written 9 days ago by
natasha.sernova • 3.4k
1
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0
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144
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Comment:
C: Rename several fasta-headers
... See the following post
https://www.biostars.org/p/53212/
and many others on its right panel,
like these ones: https://www.biostars.org/p/269611/,
https://www.biostars.org/p/174671/,
https://www.biostars.org/p/206758/, etc.
There are many awk- or sed-scripts mentioned inside,
they may give yo ...
written 9 days ago by
natasha.sernova • 3.4k
0
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1
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212
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... Oh, there are more tools! The right panel is really useful!
https://www.biostars.org/p/209529/ ...
written 13 days ago by
natasha.sernova • 3.4k
0
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1
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212
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1
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... Sergey, thank you! I saw the article in WIKI, but I didn't
pay any attention to the references. They look useful. ...
written 17 days ago by
natasha.sernova • 3.4k
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