I have two hundred no. of gene sequences whose protein structure is not known.. i want to translate appropriate protein from all the gene sequence through some software. Which software i need to use?
For each DNA sequence there are six different possibilities for protein sequences (forward and reverse, each one with three different frames), so your best bet would be finding the one which is closely matched by a protein sequence that already exists. So, as mentioned above, Blast is the way to go. I guess the best option would be doing a blastx search, on which the query is a nucleotide sequence and the search space is a protein database. If you only need to find the probable protein sequence, use nr as the database, but if you want to find a possible structure, use PDB as the database.
i am using EXPASY translate tool.. it give many results according to the frames.
Hi, the bst is in NCBI website as Adam wrote.
http://blast.ncbi.nlm.nih.gov/Blast.cgi
See left-down.
Best, A.
For each DNA sequence there are six different possibilities for protein sequences (forward and reverse, each one with three different frames), so your best bet would be finding the one which is closely matched by a protein sequence that already exists. So, as mentioned above, Blast is the way to go. I guess the best option would be doing a blastx search, on which the query is a nucleotide sequence and the search space is a protein database. If you only need to find the probable protein sequence, use nr as the database, but if you want to find a possible structure, use PDB as the database.
I am using SnapGene-Viewer for this. It is freeware.
It has a built in translate-function (for all three reading frames, 5'->3' and 3'->5' direction!) which should be ideal for your needs.
Grab it at: http://www.snapgene.com/products/snapgene_viewer/
Best of luck!
If you have no idea about where to look for genes in a sequence, as said before, BLAST would be a good idea, too...
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