Question: Locating stop codons in the incorrect reading frame
gravatar for janson.white
3.3 years ago by
United States
janson.white0 wrote:


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,



ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.3 years ago by janson.white0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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 COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k
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