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Question: Input: gene name (UCSC-style) Desired output: promoter sequences in FASTA format
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gravatar for virlana.shchuka
2.2 years ago by
virlana.shchuka • 0
virlana.shchuka • 0 wrote:

Hi everyone!

I have a list of 450 gene names for which I need to find the promoter sequences (I will later use a program to find the TF motifs in said promoter sequences). I have very little experience with bioinformatics and programming, and was wondering what is/are the most interface-friendly programs I can use to get my desired output?

Thanks!
fasta ucsc promoter extract galaxy • 739 views
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modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by virlana.shchuka • 0
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gravatar for Jennifer Hillman Jackson
2.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The UCSC's Genome Table Browser will extract this information in one step if the genome is included there (http://genome.ucsc.edu). The output can be sent to Galaxy (http://usegalaxy.org).

The tool "Get Data > UCSC Main" can be used. An example of an appropriate track would be RefSeq Genes, but you can explore others. Enter the gene names as a filter, select output as fasta, submit to filter for promoter regions. More help here or you can contact that team for more detailed usage assistance.

There are other methods, but these would involve knowing the genome coordinates of the genes and the reference genome already indexed Galaxy or loaded as a custom genome. Let us know if you need help with that by sharing more about the target genome and format of the gene names.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k
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