User: natasha.sernova

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natasha.sernova2.9k
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Posts by natasha.sernova

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Comment: C: Finding a gene of interest in contigs from a transcriptome sequencing.
... Try the following orthologous database. https://omabrowser.org/oma/home/ Select there 'general search'. Who knows, it may help you. ...
written 2 days ago by natasha.sernova2.9k
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Comment: C: Regrading the length of hypothetical pritein
... As far as I have understood, you have sequences of several or even many hypothetical proteins from some pathogen? To annotate them you need to find their known orthologous proteins. Forget for some time about their length or amounts. Try the following orthologous database: https://omabrowser. ...
written 2 days ago by natasha.sernova2.9k
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Answer: C: MSMS data: going from GI to Protein ID
... Go to NCBI-site: www.ncbi.nlm.nih.gov find 'protein' in the left menu, insert your GI-number (only number) it will give you its identifier. Your protein new identifier is can be found here https://www.ncbi.nlm.nih.gov/protein/WP_004218885.1? ...
written 11 days ago by natasha.sernova2.9k
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Comment: C: Swissprot db annotate
... A survey of best practices for RNA-seq data analysis https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728800/ DESeq vs edgeR Comparison http://www.gettinggeneticsdone.com/2012/09/deseq-vs-edger-comparison.html edgeR: differential expression analysis of digital gene expression data https://www.bioc ...
written 13 days ago by natasha.sernova2.9k
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Comment: C: Where to find archived NCBI taxonomy file
... There was NCBI-reform in 2014. Here I saved an old version. https://www.biostars.org/p/180676/ Will it be helpful to you? I am not sure. Look also here: https://www.biostars.org/p/164960/ But here the information you need is current. https://www.biostars.org/p/58872/ ...
written 4 weeks ago by natasha.sernova2.9k
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Comment: A: Get sequences for KEGG by EC and taxa
... These posts may be helpful: https://www.biostars.org/p/71737/ https://www.biostars.org/p/55962/ https://www.biostars.org/p/134892/ https://www.biostars.org/p/98922/#98923 https://www.biostars.org/p/169499/ ...
written 4 weeks ago by natasha.sernova2.9k
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Comment: A: How to get pathway ID (map ID) by pathway name
... https://www.biostars.org/p/281900/ I am sorry, you don't need it. ...
written 4 weeks ago by natasha.sernova2.9k
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Comment: C: how to get intergene coordinates for a single chromosome?
... Hopefully it may help: https://www.biostars.org/p/157836/ https://support.bioconductor.org/p/66003/ https://genome.ucsc.edu/goldenpath/help/multiRegionHelp.html https://stackoverflow.com/questions/29253412/finding-intergenic-regions ...
written 4 weeks ago by natasha.sernova2.9k
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Comment: C: Analyzing .fasta file.
... What I’ve found: The protein family was very well studied some time ago. Thare is an interesting domain here. To find it you need to aligh protein sequences with muscle or mafft. https://www.ebi.ac.uk/Tools/msa/muscle/ As to your tree, see the post below: https://www.biostars.org/p/281285/ Yo ...
written 5 weeks ago by natasha.sernova2.9k
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Comment: C: Metagenome Analysis of mycobacterium tuberculosis
... Try to use OMA-program or OrthoDB. https://omabrowser.org/standalone/ Here (link below) you can just insert your protein sequence and see what happens: https://omabrowser.org/oma/home/ OR use orthodb: http://www.orthodb.org/ They are mentioned in the following post: https://www.biostars.org/p ...
written 5 weeks ago by natasha.sernova2.9k

Latest awards to natasha.sernova

Popular Question 13 days 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 7 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 7 weeks ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Popular Question 8 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 10 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Popular Question 10 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Epic Question 13 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 14 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Scholar 16 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Popular Question 17 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 17 months ago, created a question with more than 1,000 views. For vcf to MAF to fasta
Popular Question 17 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 17 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Appreciated 17 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 18 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
Student 19 months ago, asked a question with at least 3 up-votes. For how to convert a long fasta-file into many separate single fasta sequences
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
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Teacher 21 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Scholar 21 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Scholar 21 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Scholar 21 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)

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