TY - JOUR AU - Lee, Chih AU - Huang, Chun-Hsi PY - 2013 DA - 2013/03/24 TI - LASAGNA: A novel algorithm for transcription factor binding site alignment JO - BMC Bioinformatics SP - 108 VL - 14 IS - 1 AB - Scientists routinely scan DNA sequences for transcription factor (TF) bindingsites (TFBSs). Most of the available tools rely on position-specific scoringmatrices (PSSMs) constructed from aligned binding sites. Because of theresolutions of assays used to obtain TFBSs, databases such as TRANSFAC,ORegAnno and PAZAR store unaligned variable-length DNA segments containingbinding sites of a TF. These DNA segments need to be aligned to build aPSSM. While the TRANSFAC database provides scoring matrices for TFs, nearly78% of the TFs in the public release do not have matrices available. As workon TFBS alignment algorithms has been limited, it is highly desirable tohave an alignment algorithm tailored to TFBSs. SN - 1471-2105 UR - https://doi.org/10.1186/1471-2105-14-108 DO - 10.1186/1471-2105-14-108 ID - Lee2013 ER -