Best DNA sequence analysis tool? - what is your favorite? (Nov/18/2007 )

Hi,
I was wondering what are some good online tools or downloadable software to analyze DNA sequences (restriction sites, ORF, start & stop codons, various other elements)? I have pulled out some clones by yeast two hybrid, but due to my lack of experience in molecular biology I am struggling with their analysis. Thanks for your answers!

Go to NCBI or PUBMED

Give ur serch their U can get a hook

regards
siva

Yeah, BLASTing your sequences on NCBI is the first step. Find out what they are and take it from there.

Yes, I have blasted my sequences and know what they are. Besides that, I know only where the plasmid sequence ends and where the insert begins. I want to epitope tag and subclone genes from sequenced inserts for further experiments. But how do I find the true start & stop codons of the insert? How do I find which part to cut out?

hi,

bioedit is one free software down loadable try it...........!

You can find likely genes in sequences with Orf Finder, and NCBI tool her http://www.ncbi.nlm.nih.gov/gorf/gorf.html

This will locate the stop of genes pretty accurately, but the start codon is often ambiguous (multiple ATG's, and alternative starts such as TTG or GTG). I don't know if these are eukaryotic or prokaryotic genes, but if they are prokaryotic, then you can sometimes tell by looking for the Shine-Dalgarno sequence 6 bp upstream of the start codon, consensus AGGAGG.