User: natasha.sernova
natasha.sernova • 2.5k
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Posts by natasha.sernova
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C: Problem in in alignment by muscle
... Do you still have problems? There are more different tools here.
http://www.ebi.ac.uk/Tools/msa/
I found it in this post https://www.biostars.org/p/267526/ ...
written 25 days ago by
natasha.sernova • 2.5k
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C: Problem in in alignment by muscle
... So muscle is a problem.
Try MAFFT, for example:
http://mafft.cbrc.jp/alignment/software/
I'm not sure but it may be more generous in terms of memory usage. It is.
For 64bit x86
mafft-7.271-gcc_fc6.x86_64.rpm (built on kernel 2.6)
This version uses at most x2 memory space in comparison wi ...
written 5 weeks ago by
natasha.sernova • 2.5k
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A: Problem in in alignment by muscle
... I am not quite sure, but muscle may have some limits for input file size.
What size does your input file have?
What species do you work with? In case of eukaryotes, your input may be quite large.
Do you work with nucleotides or proteins? Muscle deals with both, and you didn't tell anything about.
...
written 5 weeks ago by
natasha.sernova • 2.5k
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C: OMA current state and its updates
... Dear Christophe, THOUSAND THANKS!!! ...
written 6 weeks ago by
natasha.sernova • 2.5k
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... Dear Svetlana,
I've found and old article about that.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1613232/pdf/zpq15800.pdf
The problem is not only a protein alarge length, but also some temperature shift
or other stress conditions. ...
written 11 weeks ago by
natasha.sernova • 2.5k
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... I'm not quite sure such a database exists if you mean minimal bacterial genome size.
Look at this ald article :
http://sci-hub.cc/10.1023/B:ORIG.0000009844.90540.52
and newer articles citing it:
http://citations.springer.com/item?doi=10.1023/B:ORIG.0000009844.90540.52
...
written 11 weeks ago by
natasha.sernova • 2.5k
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... Dear Svetlana,
It's a nice and interesting bioinformatic question.
A general answer - a microorganism whose genome encodes rather long
proteins (longer then 150 amonoacids) will not survive without GroEL/GroES system.
Most enzymes are usually longer than 150 aas, so the anwer is definite NO.
BUT th ...
written 11 weeks ago by
natasha.sernova • 2.5k
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Comment:
C: OMA current state and its updates
... Dear Christophe,
Many-many thanks! If I still have some problems with OMA, I'll send you a message.
...
written 5 months ago by
natasha.sernova • 2.5k
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... Dear OMA team!
I like your program, since there are very few tools that help to find “true”-orthologs, and your papers convinced me OMA
is one of them.
I have several questions to you.
1) I don’t like to run OMA on our cluster, it takes a lot of time, uses many nodes and my colleagues do not ...
written 6 months ago by
natasha.sernova • 2.5k
• updated
5 months ago by
Christophe Dessimoz • 410
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Comment:
A: Get DrugBank data with Python
... Let's consider this Drugbank.
https://www.drugbank.ca/
There is a comprehensive guide below how to do a lot of things manually:
https://www.drugbank.ca/help
Below there is some python scripts as an artenative:
https://github.com/macarthur-lab/gene_lists
Look through the page, you will find s ...
written 6 months ago by
natasha.sernova • 2.5k
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