User: natasha.sernova

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natasha.sernova3.5k
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Posts by natasha.sernova

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Comment: A: Problem with a protein analysis
... 1) Look at this paper below. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582598/pdf/1471-2105-13-290.pdf it's for multi-label proteins, but it enumerates a lot of other tools. 2) https://www.researchgate.net/post/Is_anybody_familiar_with_subcellular_location_of_proteins The approach above is ...
written 17 days ago by natasha.sernova3.5k
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Comment: C: Best tool for bacterial genomic island prediction?
... See this article, it compares some tools of prediction. https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-9-329 The following one uses hmm-tool: https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-7-142 Am I wrong and both of them require only annotated ...
written 5 weeks ago by natasha.sernova3.5k
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Comment: C: Blasting one gene/protein against all complete genomes from bacteria and archaea
... Make a database with 'makeblastdb' from all your genomes. Then run blastx in this database. See my old post with some details: https://www.biostars.org/p/185389/#185449 To select between blastp and blastx, see the following posts: https://www.biostars.org/p/164979/#165189 https://www.biostars ...
written 5 weeks ago by natasha.sernova3.5k
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Comment: C: Multiple whole genome alignment tools ?
... You have a few eukaryotic (plant or animal) genomes,right? In general, tools for whole genomes alignment: For prokaryotes: https://www.biostars.org/p/145611/ For eukaryotes: https://www.biostars.org/p/11263/ These ENSEMBL examples (below) look informative: https://www.ensembl.org/info/genome/ ...
written 7 weeks ago by natasha.sernova3.5k
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Answer: C: What bioinformatic training?
... Some time ago I made this kind of search among 'biostars' posts and some scientific areas. It is not complete, but will provide some information. I don't like any advertisment. NGS https://go.mail.ru/search?q=bed-tools+in+NGS&fm=1&test_id=564 https://f1000research.com/articles/4-50/v2 ...
written 8 weeks ago by natasha.sernova3.5k
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Comment: C: how can i predict the interface site of RNA with protein
... I see. You need a different approach, like this one. https://github.com/xypan1232/iDeepE or this one: https://www.advancedsciencenews.com/recent-methodology-progress-of-deep-learning-for-rna-protein-interaction-prediction/ Good luck! ...
written 8 weeks ago by natasha.sernova3.5k
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Comment: C: how can i predict the interface site of RNA with protein
... 1) See this article from 2011, it compares many tools. Predicting RNA-Protein Interactions Using OnlySequence Information Usha K Muppirala1,2*, Vasant G Honavar1,3and Drena Dobbs1,2 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322362/pdf/1471-2105-12-489.pdf and update from 2017: https://link. ...
written 8 weeks ago by natasha.sernova3.5k
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Comment: C: Convert KEGG KGML files in GPML format
... A few years ago there was the following post in 'Biostars': https://www.biostars.org/p/46924/ It may help. And also look at the right panel - you will see some related posts. ...
written 9 weeks ago by natasha.sernova3.5k
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Comment: C: Bioinformatics tutor good in Python
... Why haven’t you taken a few Coursera Python courses? You can make them as intensive as you like. I would recommend Rice University and Toronto University, both provide nice Python courses in English. I met there the best Python teacher I’ve ever had. https://www.coursera.org/user/6eab68c07e3 ...
written 10 weeks ago by natasha.sernova3.5k
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Comment: C: Why fully functional protein monomer still dimerise ?
... https://www.researchgate.net/post/How_can_I_know_if_my_protein_a_monomer_or_dimer This is a wet-biology question, but it's interesting. To determine how many subunits your protein has you need analytical ultracentrifugation. The link above describes this phenomenon - protein in solution and prote ...
written 11 weeks ago by natasha.sernova3.5k

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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
Popular Question 8 months ago, created a question with more than 1,000 views. For How To Split Hhm_Db Into Hhm-Files?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: where can I get environmental bacteria genome in fasta format (as many as possib
Scholar 9 months ago, created an answer that has been accepted. For A: where can I get environmental bacteria genome in fasta format (as many as possib
Scholar 10 months ago, created an answer that has been accepted. For A: where can I get environmental bacteria genome in fasta format (as many as possib
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: where can I get environmental bacteria genome in fasta format (as many as possib
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Teacher 11 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Popular Question 12 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 13 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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Popular Question 15 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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