User: rimgubaev
rimgubaev • 40
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Posts by rimgubaev
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... 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
rimgubaev • 40
0
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1
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70
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1
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... 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: ...
written 21 days ago by
rimgubaev • 40
• updated
21 days ago by
jrj.healey • 4.9k
0
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2
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127
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... Nice one but there are only KEGG maps. ...
written 23 days ago by
rimgubaev • 40
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... 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
rimgubaev • 40
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75
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... 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 ...
written 24 days ago by
rimgubaev • 40
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2
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127
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... Thanks, will try for sure! ...
written 28 days ago by
rimgubaev • 40
2
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127
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... 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. ...
0
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118
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... There are only biomedical journals but I am planning to publish plant transcriptome dataset. ...
written 4 weeks ago by
rimgubaev • 40
0
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2
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118
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... This one is great! But It is quite expensive journal. I am looking for free journal. ...
written 4 weeks ago by
rimgubaev • 40
0
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2
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118
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... 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. ...
written 5 weeks ago by
rimgubaev • 40
Latest awards to rimgubaev
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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