SQUIRREL: Sequence QUery, Information Retrieval and REporting Library. A program package for analyzing signals in nucleic acid sequences for the VAX.
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.
Gartmann
C J
CJ
Max-Planck-Institut für Immunbiologie, Freiburg, FRG.
Grob
U
U
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