User: natasha.sernova
natasha.sernova • 3.5k
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Posts by natasha.sernova
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Comment:
A: Problem with a protein analysis
... 1) Look at this paper below.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582598/pdf/1471-2105-13-290.pdf
it's for multi-label proteins, but it enumerates a lot of other tools.
2)
https://www.researchgate.net/post/Is_anybody_familiar_with_subcellular_location_of_proteins
The approach above is ...
written 17 days ago by
natasha.sernova • 3.5k
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... See this article, it compares some tools of prediction.
https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-9-329
The following one uses hmm-tool:
https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-7-142
Am I wrong and both of them require only annotated ...
written 5 weeks ago by
natasha.sernova • 3.5k
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... Make a database with 'makeblastdb' from all your genomes.
Then run blastx in this database.
See my old post with some details:
https://www.biostars.org/p/185389/#185449
To select between blastp and blastx, see the following posts:
https://www.biostars.org/p/164979/#165189
https://www.biostars ...
written 5 weeks ago by
natasha.sernova • 3.5k
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... You have a few eukaryotic (plant or animal) genomes,right?
In general, tools for whole genomes alignment:
For prokaryotes:
https://www.biostars.org/p/145611/
For eukaryotes:
https://www.biostars.org/p/11263/
These ENSEMBL examples (below) look informative:
https://www.ensembl.org/info/genome/ ...
written 7 weeks ago by
natasha.sernova • 3.5k
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Answer:
C: What bioinformatic training?
... Some time ago I made this kind of search among
'biostars' posts and some scientific areas. It is not
complete, but will provide some information. I don't
like any advertisment.
NGS
https://go.mail.ru/search?q=bed-tools+in+NGS&fm=1&test_id=564
https://f1000research.com/articles/4-50/v2 ...
written 8 weeks ago by
natasha.sernova • 3.5k
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... I see. You need a different approach, like this one.
https://github.com/xypan1232/iDeepE
or this one:
https://www.advancedsciencenews.com/recent-methodology-progress-of-deep-learning-for-rna-protein-interaction-prediction/
Good luck! ...
written 8 weeks ago by
natasha.sernova • 3.5k
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... 1) See this article from 2011, it compares many tools.
Predicting RNA-Protein Interactions Using OnlySequence Information
Usha K Muppirala1,2*, Vasant G Honavar1,3and Drena Dobbs1,2
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322362/pdf/1471-2105-12-489.pdf
and update from 2017:
https://link. ...
written 8 weeks ago by
natasha.sernova • 3.5k
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... A few years ago there was the following post in 'Biostars':
https://www.biostars.org/p/46924/
It may help. And also look at the right panel -
you will see some related posts. ...
written 9 weeks ago by
natasha.sernova • 3.5k
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... Why haven’t you taken a few Coursera Python courses?
You can make them as intensive as you like.
I would recommend Rice University and Toronto University,
both provide nice Python courses in English. I met there
the best Python teacher I’ve ever had.
https://www.coursera.org/user/6eab68c07e3 ...
written 10 weeks ago by
natasha.sernova • 3.5k
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... https://www.researchgate.net/post/How_can_I_know_if_my_protein_a_monomer_or_dimer
This is a wet-biology question, but it's interesting.
To determine how many subunits your protein has you need analytical ultracentrifugation.
The link above describes this phenomenon - protein in solution and prote ...
written 11 weeks ago by
natasha.sernova • 3.5k
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