User: Kian

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Kian40
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Posts by Kian

<prev • 36 results • page 1 of 4 • next >
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Comment: C: What value shoould be filled at Choose Adapter Clip adapter sequences Galaxy
... Thanks Dear Ryan, Do you mean "RNA STAR" tool -Gapped-read mapper for RNA-seq data ? its needs the reference genome, as i work on the cow genome there are not this genome on the list. ...
written 6 days ago by Kian40
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What value shoould be filled at Choose Adapter Clip adapter sequences Galaxy
... I have a RNAseq data that i upload to usegalaxy and convert to Fastq format (fastq-dump). then i want to remove adapter sequence. With Clip tool in usegalaxy, there are a filed that should be fill with "Choose Adapter". how i can fill this filed? thanks ...
adapter galaxy clip choose adapter written 7 days ago by Kian40 • updated 7 days ago by Devon Ryan80k
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Comment: C: How to determine consensus sequence and conservation score for each protein?
... I see the CLUSTAL Omega, it can align the sequence the amino acids of the proteins, i should get consensus sequence by common amino acids between 3 sequence? (if 2 amino acid is common alignment, it can be in consensus sequence)? and how i can calculate conservation score? ...
written 6 weeks ago by Kian40
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Comment: C: How to determine consensus sequence and conservation score for each protein?
... May be yes, i want to comparing amino acid sequences of three protein that i have, and obtain the consensus sequence and generated homology models for these proteins. ...
written 6 weeks ago by Kian40
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Comment: C: How to determine consensus sequence and conservation score for each protein?
... Thanks for responses, If i have 3 protein sequence, i should align them for consensus sequence? how about conservation score? ...
written 6 weeks ago by Kian40
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How to determine consensus sequence and conservation score for each protein?
... How i can determine to consensus sequence and conservation score " percent of conservation" for some protein? i have some genes and i want to determine these. i know in CLC and using create alignment can do it but i want another tools for this work. Thanks ...
protein conservation score consensus sequence written 6 weeks ago by Kian40 • updated 6 weeks ago by jrj.healey4.6k
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Comment: C: Repeat elements, SINEs, LINEs, LTRs in specific regions of gene
... Thanks Dear Alex, i want to do the analysis in bos taurus8. what i should replace with hg38? ...
written 7 weeks ago by Kian40
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Comment: C: Reapet elements, SINEs, LINEs, LTRs in specific regions of gene
... Thanks Dear genomax , you mean i first in UCSC, repeat masker track, get bet output format as BED, and then take this file to BEDOPS to get the specific repeat like SINE, LINE ,.. for each region? is it true? ...
written 7 weeks ago by Kian40
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Repeat elements, SINEs, LINEs, LTRs in specific regions of gene
... Hi I have a list of more than 1000 genes, i want to calculate repeat elements like SINE, LINE, LTR frequency of these genes in several region, like in exone, intron, 3utr, 5utr, upstream, downstream. and in the specific region how many there are LINE, SINE and LTRs. chrom strand Start End ...
sine line repeat elements repeatmasker ucsc written 7 weeks ago by Kian40 • updated 7 weeks ago by Alex Reynolds24k
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Comment: C: GC count calculation of thousnds genes in several region
... Thanks, Sishuo Wang, would you please paste the link of this tool here? ...
written 7 weeks ago by Kian40

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