Search for gene sequence? - (Aug/31/2007 )
I'm performing some searches about E.coli toxin genes .
I have the primers flanking the gene hlyA.How can I find the sequence between this primers?What programm do I need?
Is there some trick to search for gene sequences only?
What's the best search strategy?
Thanks very much for your suggestions!
You can blast each sequence you have against the core nucleotide collection at Genbank. The toxin genes may not be present in the K-12 strains of lab E. coli. Find a strain which has both of your primer sequences and note the matching base numbers and accession numbers. Go to the accession number entry and set the boxes labelled Range, which start out as Begin and End to the base numbers you noted. Press Refresh. You should have the sequence between those points. If you need it in FASTA format, enter FASTA in the Display pulldown menu and press Refresh.
you might face some problems regarding the sequence that is between your primers, you should check which strain of E. coli you're using since the core genome among different strains of the same "species" of bacteria is not larger than 40%. good luck!
Thanks a lot.