Hi, I am recently using a package named HMMER to predict the binding site of the sequence. Here is my input data:
CLUSTAL O(1.2.4) multiple sequence alignment
gene1 TTTGAGTGTGTTA 13
gene2 TTTGATCTGGTTA 13
gene3 ATTGAGGTAGTTA 13
gene4 TTTGAGGCTATTG 13
I need to find the (T/A)TTGANNNNNTT(G/A) in my genome sequence, and gene1 to gene4 is also the sequence from the same genome, and I need to find that sequence from the other genes in this genome.
Now I can find about 38 binding site in my target genome; however, the score is low. I hope there is a way to increase my score.