TY - JOUR AU - Marks, Hendrik AU - Ren, Xin-Ying AU - Sandbrink, Hans AU - van Hulten, Mariƫlle CW AU - Vlak, Just M. PY - 2006 DA - 2006/06/19 TI - In silico identification of putative promoter motifs of White Spot Syndrome Virus JO - BMC Bioinformatics SP - 309 VL - 7 IS - 1 AB - White Spot Syndrome Virus, a member of the virus family Nimaviridae, is a large dsDNA virus infecting shrimp and other crustacean species. Although limited information is available on the mode of transcription, previous data suggest that WSSV gene expression occurs in a coordinated and cascaded fashion. To search in silico for conserved promoter motifs (i) the abundance of all 4 through 8 nucleotide motifs in the upstream sequences of WSSV genes relative to the complete genome was determined, and (ii) a MEME search was performed in the upstream sequences of either early or late WSSV genes, as assigned by microarray analysis. Both methods were validated by alignments of empirically determined 5' ends of various WSSV mRNAs. SN - 1471-2105 UR - https://doi.org/10.1186/1471-2105-7-309 DO - 10.1186/1471-2105-7-309 ID - Marks2006 ER -