User: natasha.sernova

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Posts by natasha.sernova

<prev • 672 results • page 1 of 68 • next >
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Comment: C: Canonical mapping UNIPROT
... I would go to this page: http://www.uniprot.org/mapping/M20180202F725F458AC8690F874DD868E4ED79B88E99245M open every abbreviation on the right and look at the protein length (on the left side) - (if it's a fragment or not), if it is a complex structure or not, if all the necessary ligands are present ...
written 20 days ago by natasha.sernova2.8k
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Comment: C: Bacterial known pathway - the easiest way to find and download 1:1 orthologs to
... Dear colleagues, THOUSAND THANKS FOR YOUR HELP!! ...
written 4 weeks ago by natasha.sernova2.8k
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Bacterial known pathway - the easiest way to find and download 1:1 orthologs to each ferment involved
... Dear all, I am studying a well known bacterial pathway. I've checked a couple of enzymes here (https://omabrowser.org/oma/) - I've found more than a thousand orthologs, but I need just orthologs in gram(+) bacteria. It's possible to do it manually, but I expect to spend a week on it. How can I do ...
genome oma written 4 weeks ago by natasha.sernova2.8k • updated 4 weeks ago by adrian.altenhoff380
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Comment: C: Upload compound to compound Database
... Concerning Pubchem : https://pubchemdocs.ncbi.nlm.nih.gov/about "the PubChem Upload Help document provides procedures and instructions on how to deposit your structure/assay" http://infotoday.com/online/sep07/Baykoucheva.shtml See the following post about Zinc-database: https://www.biostars.org ...
written 6 weeks ago by natasha.sernova2.8k
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Answer: C: NA in pathways gage values
... I've seen this point of view: http://seqanswers.com/forums/archive/index.php/t-51012.html "mSigDB gene sets are human data, not mouse. Therefore, there won’t be any human gene sets mappable or enriched in your mouse data. Please always make sure the species and gene ID types are the same for your ...
written 6 weeks ago by natasha.sernova2.8k
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Answer: A: advantages and disadvantages of 3rd generation DNA sequencing?
... See this book-chapter about it: Next-Generation Sequencing: Advantages, Disadvantages, and Future https://www.researchgate.net/publication/306431728_Next-Generation_Sequencing_Advantages_Disadvantages_and_Future There is also a WIKI-article if it's not enough: https://en.wikipedia.org/wiki/Third ...
written 6 weeks ago by natasha.sernova2.8k
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Answer: A: Recommend tools to Identify splice site regulatory elements
... Recently I have seen this one: http://www.gjcrt.org/volumes/volumes%202/5.Splice%20Site%20%20Prediction%20A%20%20Review%20%20Of%20%20Progress%20In%20Hard%20Vs%20Soft%20Computing%20Techniques.pdf ...
written 7 weeks ago by natasha.sernova2.8k
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Answer: C: FIMO: scan motif on a DNA sequence
... I just asked your question in google.com math behind motif discovery AND PWM AND HMM model I hope you will find enough math in two links I've found (they are at the bottom). If not, try to ask the same question in www.ncbi.nlm.nih.gov or www.scholar.google.com https://academic.oup.com/bioinfor ...
written 7 weeks ago by natasha.sernova2.8k
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Comment: C: FIMO: scan motif on a DNA sequence
... This paper looks like an original one: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065696/ FIMO-description: http://meme-suite.org/doc/fimo.html MEME-suite (Motif-based sequence analysis tools) scheme: http://meme-suite.org/ Some details about PWM: https://www.ncbi.nlm.nih.gov/pmc/articles/ ...
written 7 weeks ago by natasha.sernova2.8k
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Answer: A: Query regarding BLASTKOALA (KEGG) for pathway annotation
... You used the following site, am I right? http://www.kegg.jp/kegg/tool/annotate_sequence.html This site has its own limits, 2500 genes/sequences. "Query sequences – Upload a file containing multiple amino acid sequences represented by the FASTA format. The maximum number of sequences is 2500." Y ...
written 7 weeks ago by natasha.sernova2.8k

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Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Popular Question 5 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
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Scholar 7 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
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Popular Question 14 months ago, created a question with more than 1,000 views. For vcf to MAF to fasta
Popular Question 14 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
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