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Question: Locating stop codons in the incorrect reading frame
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gravatar for janson.white
3.3 years ago by
janson.white • 0
United States
janson.white • 0 wrote:

Hello,

I am new to Galaxy and hope that it will be useful for me.

I am trying to get all of the data I can from the incorrect reading frame according to all the human RefSeq transcripts. Specifically, I want to locate all the termination codons that are in the -1/+1 frames of every human transcript and see which are within 55 base pairs of the penultimate exon.

I sincerely hope someone can help me with this,

 

Thanks!!
reading frame stop codons transcript • 596 views
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modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by janson.white • 0
0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tools in the EMBOSS tool group will help to generate this type of data. Using "fuzztran" is one option. Another is using "transeq" followed by "preg". Utilize tools in the group "Convert formats" and "Text Manipulation" as needed (for example, if your data is currently in Fastq format, tools here will convert to Fasta - the required input format).

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k
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