ConsInspector 3.0: new library and enhanced functionality.

Abstract

Conslnspector (Freeh et al, 1993) is a program to scan nucleic acid sequences for matches to a pre-compiled library of transcription factor binding sites. The program carries out an extensive examination of binding site candidates; the real sequence is compared with randomly shuffled versions and sequence regions surrounding the conserved binding site are included in the analysis (default 40 bp upstream and 40 bp downstream of the highly conserved core sequence). This feature distinguishes the program from other methods available for the identification of transcription factor binding sites which are restricted to the binding sites: SIGNAL SCAN (Prestridge, 1991, 1996; Prestridge and Stormo, 1993), MATRIX SEARCH (Chen et al, 1995) and Matlnspector (Quandt et al, 1995a). Recently, we showed the quality scores (Q-scores) assigned by Conslnspector to correlate to some extent with biological functionality (Quandt et al, 1995b). Release 3.0 of Conslnspector, with enhanced performance and a considerably extended library of consensus profiles, is available now at ftp://ariane.gsf.de/pub/ or http://www.gsf.de/biodv/. The program Conslnd (Freeh et al, 1993) has been used to compile the library of consensus profiles. The library now encompasses 37 consensus profiles (Release 1.0: 12, Release 2.1: 17 consensus profiles) and is separated into four groups (Table I). The extended weight matrices were deduced from experimentally confirmed binding sequences selected from the TRANSFAC database (Wingender et al, 1996) or directly from the literature. Most consensus profiles of the original library have been improved by the inclusion of additional sequences. Consensus profiles have been compiled from a minimum of nine sequences (Table I). The analysis of DNA sequences for transcription factor binding sites with Conslnspector has improved since Release 1.0: