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