User: natasha.sernova

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natasha.sernova2.4k
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Posts by natasha.sernova

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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 1 day ago by natasha.sernova2.4k
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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 days ago by natasha.sernova2.4k
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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 8 days ago by natasha.sernova2.4k
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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 17 days ago by natasha.sernova2.4k
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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 17 days ago by natasha.sernova2.4k
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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 17 days ago by natasha.sernova2.4k
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Comment: C: How to transform locus_tags to protein sequences (bacteria)
... Thanks for your reply! I tried it and started with *.faa files, I hoped it's a solution. It turned out there is no locus_tags in their headers. I looked at a bacterium from 2016. I looked at this post. https://www.biostars.org/p/233290/. I don't have a gene symbol, just locus_tag. Right now I d ...
written 18 days ago by natasha.sernova2.4k
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How to transform locus_tags to protein sequences (bacteria)
... Dear ALL, Is there a direct way to transform several bacterial protein locus_tags to the protein sequences? I’ve found a few posts about genes, locus_tags and biopython. https://www.biostars.org/p/233290/ https://www.biostars.org/p/94164/ https://www.biostars.org/p/110284/, but I need protein seq ...
locus bacteria eutils written 18 days ago by natasha.sernova2.4k • updated 17 days ago by pure_reason10
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Answer: A: Why some questions in OPEN section of the Biostars.org have "(Closed)" at the be
... Dear colleagues, As far as I have understood, a question may be closed by a moderator if the topic doesn't relate to bioinfornatic area. If the author of the question provides some additional details and proves it does relate to bioinformatics, it won't be closed. If this question is not complete a ...
written 29 days ago by natasha.sernova2.4k
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Comment: C: GC Content and GC Skew are not showing in BRIG image
... You use it for some bacteria, right? It's easy to learn GC-content from Genbank, and GC-skew from this site below or its update: http://www2.unil.ch/comparativegenometrics/index.html By the way, the authors of this old paper below used the program and didn't complain, right? http://bmcgenomics. ...
written 4 weeks ago by natasha.sernova2.4k

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Teacher 14 days ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Scholar 10 weeks ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
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 3 months ago, created a question with more than 1,000 views. For vcf to MAF to fasta
Popular Question 3 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 3 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
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Commentator 4 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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