I need to identify certain sequences and look out for a pattern in my cDNA. Can anyone suggest me a software that can detect 3'UTRs etc?
Maybe you can simply use the curated mRNA datasets from UCSC or RefSeq genes? You can download these files from UCSC's Table Browser. Transcription start/end and coding sequence start/end coordinates are given. 3'UTRs are simply the sequence between the CDS end + 1bp to the transcription end coordinate. I don't think you need to rely on predicting exons, and instead can use the information on known coding sequences to find 3'UTR for each gene.
Edit: in fact, the Table Browser allows you to output the data as a bed file and then select for only the 3' UTR coordinates, saving you a step.
Hi Amruta,
you can either submit your sequence of interest here http://itbtools.ba.itb.cnr.it/utrscan or directly look for your gene of interest in their database (http://utrdb.ba.itb.cnr.it/asearch). I hope it will help.
I've used Dr. Cohen's method before and it works perfectly :)
good luck
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