User: konstantinkul

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Posts by konstantinkul

<prev • 30 results • page 1 of 3 • next >
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Forum: Clustering proteins by Pfam annotation
... Hi all, What do you think is it possible to cluster annotated proteins (using InterProScan) by (for example) Pfam IDs? The issue is that each protein may have several Pfam IDs (several domains, families etc). This is just an idea of clustering by functional annotation, I tried Orthotomcl, Spectral ...
forum clustering pfam written 1 day ago by konstantinkul70
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Comment: C: Biopython / Python for genomics data analysis online courses
... If you are starting from scratch in programming, you should start from foundations of Python programming and do not pay attention to bioinformatics aspects. I think on this stage you should just feel that you write the code more or less freely (of course everybody googling or stack overflowing, but ...
written 5 months ago by konstantinkul70
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Comment: C: Interproscan GO terms results expalnation
... Ok, I got it! Thanks a lot! ...
written 9 months ago by konstantinkul70
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Interproscan GO terms results explanation
... Hi all, I am new in InterPro scan as well as in genome annotation. I need to classify genes by GO terms to obtain a general table "GO Terms Classification Count Results" Could you please explain me one thing. When I run Interproscan with '-goterms' option it generated for me such output where seve ...
genome gene written 9 months ago by konstantinkul70 • updated 9 months ago by Michael Dondrup44k
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Comment: C: Pangenome Analysis using Roary tool
... Open file gene_presence_absence.csv in Excel and select all rows where 'No. isolates' equal to a number of analyzed genomes (strains). These genes will be core genes. ...
written 12 months ago by konstantinkul70
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Answer: A: Pangenome Analysis using Roary tool
... Install Roary and Prokka Go to path with fasta genomes > cd path/to/fastas/ Annotate fasta genomes with Prokka > for i in *.fa; do prokka $i --addgenes --locustag ${i%.*} --force --cpus 32; done Collect all GFF files from each genome folder to tm folder > mkdir t ...
written 12 months ago by konstantinkul70
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Answer: A: Phylogenetic tree for viruses
... Make MSA with mafft (http://mafft.cbrc.jp/alignment/server/) Find the best substitution model with MEGA Create phylogenetic tree using ML (maximum likelihood) methods with model defined in MEGA ...
written 12 months ago by konstantinkul70
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GenePrimp error: Illegal division by zero at BPlite.pm line 283, <$__ANONIO__> line 400764.
... Hello, Did anybody has the error while the GenePrimp (http://www.nature.com/nmeth/journal/v7/n6/full/nmeth.1457.html) parsing the Blastp output at the first stage of analysis. I have the same issue by analysis both the gbk file from ncbi and the gbk file produced by Prokka. I also tested the differ ...
software error gene genome written 14 months ago by konstantinkul70
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Comment: C: Genome coverage against normalized average depth
... Thank you for your reply. I have similar doubts about "theoretical" line. Let me explain my pipeline 1. I create coverage column for each position of ref genome `$ bedtools coverage -abam some.bam -b fasta.tab -d > cov.txt` extrat last column `cut -f 6 cov.txt > genome_depth` 2. In R `tab ...
written 17 months ago by konstantinkul70
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Genome coverage against normalized average depth
... Hello! Does anybody dealt with this type of graph "A plot of genome coverage against normalized average depth" http://prntscr.com/df9wmc. I really need it for optimization of procedures of WGS. I was trying to figure it out how to generate it, but I couldn't. The description in methods section was ...
R next-gen written 17 months ago by konstantinkul70 • updated 17 months ago by Brian Bushnell15k

Latest awards to konstantinkul

Popular Question 8 months ago, created a question with more than 1,000 views. For Convert fasta alignment to Vector NTI *.apr format
Popular Question 14 months ago, created a question with more than 1,000 views. For Pipeline For Amplicons Analysis
Popular Question 14 months ago, created a question with more than 1,000 views. For Pipeline For Amplicons Analysis
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Popular Question 3.7 years ago, created a question with more than 1,000 views. For Miseq Pair-End Library De-Novo Assembly - Broken Pairs?

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