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. 1991 Nov 11;19(21):6033–6040. doi: 10.1093/nar/19.21.6033

SQUIRREL: Sequence QUery, Information Retrieval and REporting Library. A program package for analyzing signals in nucleic acid sequences for the VAX.

C J Gartmann 1, U Grob 1
PMCID: PMC329063  PMID: 1945887

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.

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Selected References

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