User: natasha.sernova

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natasha.sernova3.4k
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Posts by natasha.sernova

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Comment: C: Searching for a sequence within another sequence Biopython
... As far as I have understood, a person who asked a question was going to get a position of some fragment in a larger sequence. But that particular fragment may differ a little bit from a real plasmid sequence. The matrix I suggested a few days ago is an ancient approach, but it would help. The a ...
written 2 hours ago by natasha.sernova3.4k
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Comment: C: Searching for a sequence within another sequence Biopython
... I 've seen this post that should help to find identical residues. https://www.biostars.org/p/318684/#319376 I hope it may help you. ...
written 3 hours ago by natasha.sernova3.4k
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Comment: C: Searching for a sequence within another sequence Biopython
... The sequence you've provided is not a whole plasmid sequence, right? It looks like some gene upstream. In this or similar cases you have to find orthologous gene upstreams (the same gene from close species), find out, how your site looks like there, then make a PWM (position weight matrix) - ...
written 1 day ago by natasha.sernova3.4k
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Comment: C: CpG islands prediction
... See this post from 'Biostars': https://www.biostars.org/p/79046/ https://www.biostars.org/p/57380/ A few other articles: 1)https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2883304/ Biostatistics. 2010 Jul; 11(3): 499–514. Redefining CpG islands using hidden Markov models Hao Wu, Brian Caffo, Harris A ...
written 3 days ago by natasha.sernova3.4k
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Comment: C: Searching for a sequence within another sequence Biopython
... It seems you need a simple python script like this one below: """ string: AGTGTTAAGAAGTCCGT and the recognition site is something like: AAGAAG """ def posit_in_seq(string,site): len_site = len(site) if site in string: for i in range (0, l ...
written 3 days ago by natasha.sernova3.4k
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Comment: C: scRNA-seq non-technical article
... I am not sure if it's possible to make the topic really popular. These articles below look clear and understandable. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications Ashraful Haque, Jessica Engel, Sarah A. Teichmann and Tapio Lönnberg Genome Medic ...
written 3 days ago by natasha.sernova3.4k
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Comment: C: Suggestions for: Annotating the genome using analysis of genomic/ proteomic data
... There are a lot of posts in "Biostars" about it. Start with this one: https://www.biostars.org/p/325071/ Then look at the right panel of the post above, you will see a lot of similar posts. If it's not enough, go to the upper left corner, select LATEST and type your question to the empty string ...
written 9 days ago by natasha.sernova3.4k
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Comment: C: Rename several fasta-headers
... See the following post https://www.biostars.org/p/53212/ and many others on its right panel, like these ones: https://www.biostars.org/p/269611/, https://www.biostars.org/p/174671/, https://www.biostars.org/p/206758/, etc. There are many awk- or sed-scripts mentioned inside, they may give yo ...
written 9 days ago by natasha.sernova3.4k
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Comment: C: RNA-secondary structure prediction software (T-boxes, riboswitches and attenuato
... Oh, there are more tools! The right panel is really useful! https://www.biostars.org/p/209529/ ...
written 13 days ago by natasha.sernova3.4k
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Comment: C: RNA-secondary structure prediction software (T-boxes, riboswitches and attenuato
... Sergey, thank you! I saw the article in WIKI, but I didn't pay any attention to the references. They look useful. ...
written 17 days ago by natasha.sernova3.4k

Latest awards to natasha.sernova

Appreciated 18 days ago, created a post with more than 5 votes. For how to convert a long fasta-file into many separate single fasta sequences
Teacher 22 days 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
Autobiographer 10 weeks ago, has more than 80 characters in the information field of the user's profile.
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
Popular Question 3 months ago, created a question with more than 1,000 views. For How To Split Hhm_Db Into Hhm-Files?
Scholar 5 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 5 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
Teacher 5 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 5 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
Popular Question 7 months ago, created a question with more than 1,000 views. For Tools to find the unique proteins (without orthologs) in a bacterial taxon
Teacher 7 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
Popular Question 9 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 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
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 Tools to find the unique proteins (without orthologs) in a bacterial taxon
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Popular Question 18 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 20 months ago, created an answer that has been accepted. For A: dN/dS ratio (omega)
Popular Question 20 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 23 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 2.0 years ago, created an answer with at least 3 up-votes. For A: dN/dS ratio (omega)
Scholar 2.2 years ago, created an answer that has been accepted. For A: dN/dS ratio (omega)

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