title: SQUIRREL: Sequence QUery, Information Retrieval and REporting Library. A program package for analyzing signals in nucleic acid sequences for the VAX.
abstract: A computer tool is described for comparison, analysis and search of genetic signals. The method is based on sequence consensus matrices. It assumes that a genetic signal (such as a promoter, enhancer or whatever) is composed of several signal blocks separated from each other by variable distances. A set of programs is presented to perform the analysis. The result of such an analysis is a description of the investigated signal including matrices for each signal block, distances between each block and distribution of the values. Programs are provided to search for a signal using results from previous analysis. The method is able to align large sets of sequences within a few minutes and to check the quality of the alignment. An analysis of E.coli promoters is provided as an example.
authors.affiliation: Max-Planck-Institut für Immunbiologie, Freiburg, FRG.
authors.forename: C J
authors.initials: CJ
authors.lastname: Gartmann
authors.forename: U
authors.initials: U
authors.lastname: Grob
mesh_terms: D000465:Algorithms; D001483:Base Sequence / Q000235:genetics*; D016384:Consensus Sequence / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D015723:Gene Library; D007256:Information Systems; D011401:Promoter Regions, Genetic / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D012984:Software