User: rimgubaev

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rimgubaev40
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Posts by rimgubaev

<prev • 12 results • page 1 of 2 • next >
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Answer: A: How to extract all promoter regions in multi-fasta format from genome using GFF?
... Finally, I've solved this problem by combining samtools, bedtools as well as custom R script. The pipline placed into bash script [here](https://github.com/RimGubaev/extract_promoters). ...
written 10 days ago by rimgubaev40
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Are there some ways to extract information in tabular format from text with regular pattern?
... Hello everyone! I have an output from [NsiteM](http://www.softberry.com/berry.phtml?topic=nsitem&group=programs&subgroup=promoter) which represents a text with promoter analysis results. The text has a regular pattern: 1. QUERY: Gene1 Length of Query Sequence: ...
nsitem promoter analysis text mining written 21 days ago by rimgubaev40 • updated 21 days ago by jrj.healey4.9k
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Comment: C: Could somebody suggest free pathway visualization tool for omics data from plant
... Nice one but there are only KEGG maps. ...
written 23 days ago by rimgubaev40
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Comment: C: How to search cis-regulatory elemens using promoter multifasta from non-model pl
... I am interested in regulatory elements that may affect gene expression under certain condition. For example the presence of several ABREs (Abscisic acid responsive elements) within promoter region indicate that this gene is likely to be up-regulated under unfavorable conditions or ABA treatment. In ...
written 23 days ago by rimgubaev40
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How to search cis-regulatory elemens using promoter multifasta from non-model plant?
... I need to find cis-regulatory elements in multifasta file with promoters of *Nicotiana tabacum*. I've tried PlantPAN and PlantTFDB but these programs output quite useless information on TF families that binds to a certain region. Nice one is [PLACE](https://sogo.dna.affrc.go.jp/cgi-bin/sogo.cgi?lang ...
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Comment: C: Could somebody suggest free pathway visualization tool for omics data from plant
... Thanks, will try for sure! ...
written 28 days ago by rimgubaev40
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Could somebody suggest free pathway visualization tool for omics data from plants?
... I've tried to visualize my data using MapMan and KEGG Mapper but the quality of their pathway diagrams is much to be desired. I've also used BioCyc which is nice however today it requires a subscription. ...
pathways vizualization rna-seq written 29 days ago by rimgubaev40 • updated 24 days ago by bigmawen270
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Comment: C: Are there any journals that accept short transcriptome announcements?
... There are only biomedical journals but I am planning to publish plant transcriptome dataset. ...
written 4 weeks ago by rimgubaev40
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Answer: A: Are there any journals that accept short transcriptome announcements?
... This one is great! But It is quite expensive journal. I am looking for free journal. ...
written 4 weeks ago by rimgubaev40
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Are there any journals that accept short transcriptome announcements?
... I would like to know if there are journals that accept short communications c.a. 3-5 pages on transcriptome with supplementary data (raw reads, expression data, pathway enrichment data e.t.c.) and short discussion of the results. ...
rna-seq written 5 weeks ago by rimgubaev40

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Teacher 10 days ago, created an answer with at least 3 up-votes. For A: How to extract all promoter regions in multi-fasta format from genome using GFF?

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