Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements

Background: Many DNA regulatory elements occur as multiple instances within a target promoter. Gibbs sampling programs for finding DNA regulatory elements de novo can be prohibitively slow in locating all instances of such an element in a sequence set. Results: We describe an improvement to the A-GLAM computer program, which predicts regulatory elements within DNA sequences with Gibbs sampling. The improvement adds an optional "scanning step" after Gibbs sampling. Gibbs sampling produces a position specific scoring matrix (PSSM). The new scanning step resembles an iterative PSI-BLAST search based on the PSSM. First, it assigns an "individual score" to each subsequence of appropriate length within the input sequences using the initial PSSM. Second, it computes an E-value from each individual score, to assess the agreement between the corresponding subsequence and the PSSM. Third, it permits subsequences with E-values falling below a threshold to contribute to the un...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Kannan Tharakaraman, Leonardo Mariño-Ramírez, Sergey Sheetlin, David Landsman, John L. Spouge
• Keywords: BMCBI 2006, DNA Regulatory Elements, Regulatory Element, Scanning Step