Analysis and prediction of baculovirus promoter sequences

Consensus patterns of baculovirus sequences upstream from the translational initiation sites have been analyzed and a web tool, Local Alignment Promoter Predictor (LAPP), for the prediction of baculovirus promoter sequences has also been developed. Potential consensus sequences, i.e., TCATTGT, TCTTGTA, CTCGTAA, TCCATTT and TCATT plus TCGT in approximately 30 bp spacing context, have been found in baculovirus promoter regions, in addition to well-characterized late and early promoter elements G/T/ATAAG and TATAA, which is accompanied about 30-bp downstream by a transcriptional initiation sequence CAGT or CATT. Promoter prediction is performed by a dynamic programming algorithm based on maximal segment pair measure with scores above some cutoff against each sequence in a refined promoter database. The algorithm was able to discriminate between promoter and non-promoter sequences in a test set of baculovirus sequences with prediction specificity and sensitivity superior to that using five other eukaryotic promoter recognition programs available on the Internet. A web server that implements the LAPP with continually updated promoter database is freely available at http://life.zsu.edu.cn/LAPP/.