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

C J Gartmann·U Grob
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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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AlgorithmsBase SequenceConsensus SequenceEscherichia coliGene LibraryInformation SystemsPromoter Regions, GeneticSequence AlignmentSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

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BibTeXRIS

C J Gartmann, U Grob. 1991-11-11. SQUIRREL: Sequence QUery, Information Retrieval and REporting Library. A program package for analyzing signals in nucleic acid sequences for the VAX.. https://doi.org/10.1093/nar%2F19.21.6033

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