User: natasha.sernova

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natasha.sernova2.5k
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Posts by natasha.sernova

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Comment: C: Can a bacterial microogranism survive without GroEL protein?
... 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 18 days ago by natasha.sernova2.5k
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Comment: C: How can I find a minimal bacterial protein dataset ?
... 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 20 days ago by natasha.sernova2.5k
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Answer: C: Can a bacterial microogranism survive without GroEL protein?
... 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 20 days ago by natasha.sernova2.5k
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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 3 months ago by natasha.sernova2.5k
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OMA current state and its updates
... 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 ...
orthologs oma bacteria update written 3 months ago by natasha.sernova2.5k • updated 3 months ago by Christophe Dessimoz390
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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 4 months ago by natasha.sernova2.5k
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Comment: A: Species identification via gilist
... Hello! I see a couple of possible problems: 1) your gi.list file is too large, 3 Gb. BLAST has some limits as far as I remember. 2) BLAST cannot find the file since you put it here: http://bioinfo.cs.ccu.edu.tw/CCU_bioinf/bacteria.taxid.gi.txt If you run blast ih the same directory, it's OK 3) ...
written 4 months ago by natasha.sernova2.5k
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Comment: C: How to transform locus_tags to protein sequences (bacteria)
... No, that's perfect! Thousand thanks! I meant, NCBI site does not recognize locus_tags from old gbk-files. I don't need their old versions, but they are reachable from old ncbi-versions, I hope. ...
written 4 months ago by natasha.sernova2.5k
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Comment: C: How to transform locus_tags to protein sequences (bacteria)
... Thank you for your question! It turned out that old locus_tags are not recognized in ncbi-site. This is a modern example: SEEE7246_00015 SEEE7246_00040 SEEE7246_00050 SEEE7246_00075 SEEE7246_00080 All of them have some corresponding protein sequences. But how to find them automatically? Tha ...
written 4 months ago by natasha.sernova2.5k
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Comment: C: How to transform locus_tags to protein sequences (bacteria)
... My bacterial *.faa - files do not have locus-tags in their headers. It may be some exception, but they don't. I have a couple of ideas, To search GPFF-files. It's a new version of *.gbk files, they have both lovus-tag and protein sequence somewhere nearby. But I have only a list of locus-tags and ...
written 4 months ago by natasha.sernova2.5k

Latest awards to natasha.sernova

Popular Question 18 days ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Scholar 18 days ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Epic Question 3 months ago, created a question with more than 10,000 views. For how to convert a long fasta-file into many separate single fasta sequences
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Scholar 6 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Popular Question 6 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Popular Question 6 months ago, created a question with more than 1,000 views. For vcf to MAF to fasta
Popular Question 6 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Scholar 7 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Appreciated 7 months ago, created a post with more than 5 votes. For how to convert a long fasta-file into many separate single fasta sequences
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: How to find a conserved regions for a protein by phylogentic analysis tree
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