Hello everyone,
I want know the program that I can use to analyze my Data sequence of part of cDNA inserted on plasmid to get information about the 5 untranslated region of the mRNA, to get more information about promoter, exon and intron. I don not know how to use the sequence for analysis .
Thanks for your help,
Zeinab
If you have a lot of sequences, the command line program TransDecoder may be useful for defining the portions of the cDNA that are coding or UTR. If you have a genome as well, this can be extended to identify the introns and exons.
If you want to analysis intron, exon and UTR region, then Gene Display Server is a good tool.
Hi Zeinab,
Did you analyze your sequences first and did all the first steps (trimming adapters, vector and low quality regions; assembly all sequences into contigs)?
You can first do BLASTn and BLASTx analysis to annotate your sequences. Then you can look for coding regions as Warren said and conservative dommains; align your sequences in a reference genome (with a splice junction mapper); and others downstream analysis depending what are your aims.
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