User: ivan.antonov

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ivan.antonov90
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Moscow, Russia
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Posts by ivan.antonov

<prev • 16 results • page 1 of 2 • next >
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Answer: A: Could not find rRNA genes (28S, 18S, 5.8S and 5S) in human_genes.gtf file?
... Hi, guys! I believe that some 45S genes are now present in the hg38 human reference genome, for example: https://www.ncbi.nlm.nih.gov/gene/106631777 Here is the location in UCSC GenomeBrowser -- chr21:8,433,222-8,446,572 http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr21%3A84332 ...
written 16 months ago by ivan.antonov90
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Answer: A: Count the number of sequences in fasta file using perl
... You can do many things in UNIX command line using Perl and "wc". Counting the number of sequences: grep '>' INPUT.fasta | wc -l --- Counting the total length of all sequences: grep -v '>' INPUT.fasta | perl -pe 's/[\n\r]//g' | wc -c --- List of all sequence lengths: cat INPU ...
written 2.2 years ago by ivan.antonov90
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Comment: C: How to visualize gene structure of a (prokaryotic) locus?
... This is just perfect -- thanks a lot! ...
written 2.2 years ago by ivan.antonov90
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Comment: C: How to visualize gene structure of a (prokaryotic) locus?
... Thanks -- DNAFeaturesViewer and GenomeDiagrams python libs look like what I need:) ...
written 2.2 years ago by ivan.antonov90
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Comment: C: How to visualize gene structure of a (prokaryotic) locus?
... Thanks for the link! ...
written 2.2 years ago by ivan.antonov90
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Comment: C: How to visualize gene structure of a (prokaryotic) locus?
... Yeah, something like GFF format. I can prepare a list of genomic coordinates for the genes of interest in any format... ...
written 2.2 years ago by ivan.antonov90
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Comment: C: How to visualize gene structure of a (prokaryotic) locus?
... Thanks for the response! It may be difficult to accurately visualize the gene lengths and intergenenic distances by hand, though.. ...
written 2.2 years ago by ivan.antonov90
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How to visualize gene structure of a (prokaryotic) locus?
... Hello, guys! I was wondering, how an image like this can be automatically (programmatically) generated from the initial data in a text file? ![enter image description here][1] The figure is taken from https://www.ncbi.nlm.nih.gov/pubmed/29168502 Could anyone recommend a good R package for this? ...
genome R visualisation gene python written 2.2 years ago by ivan.antonov90 • updated 2.2 years ago by h.mon31k
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Comment: C: How to draw a phylogenetic tree together with a genome locus structure?
... Yes, Brice -- nice note about the font! Thank you once again for the answer:) Ivan ...
written 4.1 years ago by ivan.antonov90
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How to draw a phylogenetic tree together with a genome locus structure?
... Hello, I am wondering, what tool/R-package can be used to draw this type of tree (preferably, programmatically)? ![enter image description here][1] The image is taken from: https://www.ncbi.nlm.nih.gov/pubmed/26773003 [1]: http://ivanya.com/tmp/2016/1024.tree.png ...
draw tree tool written 4.1 years ago by ivan.antonov90 • updated 4.0 years ago by Guangchuang Yu2.4k

Latest awards to ivan.antonov

Supporter 10 months ago, voted at least 25 times.
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Count the number of sequences in fasta file using perl
Popular Question 4.1 years ago, created a question with more than 1,000 views. For How to draw a phylogenetic tree together with a genome locus structure?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For What tools were used to draw these phylogenetic trees?

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