User: natasha.sernova

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natasha.sernova2.6k
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Posts by natasha.sernova

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Comment: C: How to convert a .gbff to the .gbk using batch method (to do it computationally
... Thank you very much, it's a good idea! ...
written 4 days ago by natasha.sernova2.6k
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How to convert a .gbff to the .gbk using batch method (to do it computationally for several bacteria)
... Dear all, https://www.biostars.org/p/180676/ From the post above I know how to reach .gbff-files of all bacteria. When I unzip any genomic.gbff.gz file, I get genomic.gbff file But it is multilocus file. Uniprot Ugene makes it single locus .gbk file, suitable for any software. But how to do it ...
genome .gbff .gbk written 4 days ago by natasha.sernova2.6k
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Answer: C: How to extract known pathways from protein protein interaction network?
... See my answer to the following post: https://www.biostars.org/p/280536/#282679 it gives KEGG links. There are a lot of papers about ppi, try to search KEGG. I’ve provided some necessary links in my post above: But it is not quite clear whose proteins you study. STRING may also be helpful. Th ...
written 10 days ago by natasha.sernova2.6k
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Answer: C: Pathway annotation using sequence alignment
... To find bacterial genomes (there are much more now) see the post below: https://www.biostars.org/p/180676/ To look for KEGG-pathways see these recent papers: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210567/pdf/gkw1092.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5584762/ There are thou ...
written 14 days ago by natasha.sernova2.6k
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Comment: C: genome databases of ancient bacteria, in particular ancient gram-positive ones
... Yes! I would like to find a database or whatever it is with some firmicute genomes of many generations. But I need to have a starting genome, a middle point genome and a final genome. I am afraid it has not been done yet, it implies a hard wet-lab work. ...
written 28 days ago by natasha.sernova2.6k
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Comment: C: genome databases of ancient bacteria, in particular ancient gram-positive ones
... Thank you for your question! I would be happy to be able to compare bacterial genomes from the 1st and several hundred generation. I found less than 10 papers mentioning it, and most are about E.coli only. But I need some information about gram-positive bacteria. ...
written 28 days ago by natasha.sernova2.6k
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Comment: C: genome databases of ancient bacteria, in particular ancient gram-positive ones
... Thank you very much, Kevin! That's great! ...
written 28 days ago by natasha.sernova2.6k
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Comment: C: genome databases of ancient bacteria, in particular ancient gram-positive ones
... Exactly! I am just trying to find out if they do indeed exist. There are thousands of bacterial papers, this particular aspect may not be essential for the authors. That's why I've asked the question - someone could read someting about. Yesterday I saw an article about many E.coli generations. But I ...
written 28 days ago by natasha.sernova2.6k
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Comment: C: genome databases of ancient bacteria, in particular ancient gram-positive ones
... No, I never used this approach. It looks very nice, thank you! Usually I use the information from this post (https://www.biostars.org/p/180676/) to find some bacterial genomes. But what about time scale? How to distinguish between current strains and ancient strains? Firmicutes are not human-frien ...
written 29 days ago by natasha.sernova2.6k
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genome databases of ancient bacteria, in particular ancient gram-positive ones
... Dear all, I am looking for some current databases of ancient firmicute ganomes. I saw 7 posts in Biostars. I hope someone may have some new information. TYVM! ...
genome database firmicutes ancient bacteria written 4 weeks ago by natasha.sernova2.6k • updated 29 days ago by Kevin Blighe7.2k

Latest awards to natasha.sernova

Popular Question 12 weeks 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 4 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 4 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Epic Question 7 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 8 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Scholar 10 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Popular Question 11 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 11 months ago, created a question with more than 1,000 views. For vcf to MAF to fasta
Popular Question 11 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 11 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
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Commentator 12 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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