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Finding ORFs in Multiple Seqeunces

Finding ORFs in Multiple Seqeunces - Bioinformatics

Finding ORFs in Multiple Seqeunces - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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Old 11-30-2008, 11:28 PM
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Default Finding ORFs in Multiple Seqeunces



Is there any such program that you don't have to input the sequence in one at a time? And then you can extract the DNA sequence?
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Old 12-03-2008, 05:01 PM
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Default Re: Finding ORFs in Multiple Seqeunces

Im not totally sure this is what you mean, but you can try googling Exon Primer. You input the cDNA sequence and the sequence of the gene. It finds all the separate exons in the gene sequence and designs primers around them.
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Old 12-03-2008, 11:04 PM
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Default Re: Finding ORFs in Multiple Seqeunces

Sorry let me clarify. I have about 35 mRNA seqeunces. Of which I only want the protein-coding sequence (or open reading frame). The only program that can do this is ORF finder but this only one sequences at a time. I was wondering, simply for convenience whether a program existed that allowed me to enter multiple sequences at a time, rather than one-by-one.
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Old 02-03-2009, 07:38 AM
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Default Re: Finding ORFs in Multiple Seqeunces

This task can be implemented with a couple of clicks in UGENE Workflow Designer plugin. This tool is free.

Run it, select Tools->Workflow Designer -> Basic Analsyis -> ORF marker.

Now link it with Generic Sequence Reader as input and Genbank Writer as an output.
After you run it you will have ORFs stored in Genbank format files as annotations to the original sequence.
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