Computer Analysis of Sequence Data, Part I - Annette M Griffin

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Résumé :
DNA sequencing has become increasingly efficient over the years, resulting in an enormous increase in the amount of data gen- ated. In recent years, the focus of sequencing has shifted, from being the endpoint of a project, to being a starting point. This is especially true for such major initiatives as the human genome project, where vast tracts of DNA of unknown function are sequenced. This sheer volume of available data makes advanced computer methods ess- tial to analysis, and a familiarity with computers and sequence ana- sis software a vital requirement for the researcher involved with DNA sequencing. Even for nonsequencers, a familiarity with sequence analysis software can be important. For instance, gene sequences already present in the databases can be extremely useful in the design of cloning and genetic manipulation experiments. This two-part work on Analysis of Data is designed to be a practical aid to the researcher who uses computers for the acquisition, storage, or analysis of nucleic acid (and/or p- tein) sequences. Each chapter is written such that a competent sci- tist with basic computer literacy can carry out the procedure successfully at the first attempt by simply following the detailed pr- tical instructions that have been described by the author. A Notes section, which is included at the end of each chapter, provides advice on overcoming the common problems and pitfalls sometimes enco- tered by users of the sequence analysis software. Software packages for both the mainframe and personal computers are described.

Sommaire:
Computer Analysis of Sequence Data.- GCG: Fragment Assembly Programs.- GCG: Drawing Linear Restriction Maps.- GCG: Drawing Circular Restriction Maps.- GCG: Displaying Restriction Sites and Possible Translations in a DNA Sequence.- GCG: Assembly of Sequences into New Sequence Constructs.- GCG: Comparison of Sequences.- GCG: Production of Multiple Sequence Alignment.- GCG: Database Searching.- GCG: Pattern Recognition.- GCG: Translation of DNA Sequence.- GCG: Analysis of Protein Sequences.- GCG: The Analysis of RNA Secondary Structure.- GCG: Preparing Sequence Data for Publication.- MicroGenie: Introduction and Restriction Enzyme Analysis.- MIicroGenie: Shotgun DNA Sequencing.- MicroGenie: Translation.- MicroGenie: Protein Analysis.- MicroGenie: Homology Searches.- PC/GENE: Sequence Entry and Assembly.- PC/GENE: Restriction Enzyme Analysis.- PC/GENE: Translation and Searches for Protein Coding Regions.- PC/GENE: Sequence Comparisons and Homologies.- PC/GENE: Database Searches.- PC/GENE: Searches for Functional Sites in Nucleic Acids and Proteins.- Using the FASTA Program to Search Protein and DNA Sequence Databases.- Converting Between Sequence Formats.- Obtaining Software via INTERNET.- Submission of Nucleotide Sequence Data to EMBL/GenBank/DDBJ.