Includes bibliographical references and indexes.

A. Author's profile -- B. Dedication -- C. Preface -- D. Acknowledgements -- A. Part one: principles -- 1. Web-based sequence analysis: blast i -- Basic local alignment search tool (blast) -- The purpose of blast -- Terminology -- Blast analysis -- Blast2 -- Automated alignments with perl -- Assignments -- Appendix i -- References -- 2. Web-based sequence analysis: blast ii -- Basic local alignment search tool (blast) -- Scoring matrices -- Pam or per cent accepted mutation matrices -- Blosum (blocks substitution matrices) -- The relationship between blosum and pam substitution matrices -- Working of the blast algorithm -- A practical blastn exercise -- Explanation of the blast output -- Advanced blastn -- Biological analysis of blastn: cystic fibrosis -- Automating blast analyses with perl -- Assignments -- 3. Web-based sequence analysis: blast iii -- Standalone blast -- Configuring blastall -- Downloading databases from ncbi -- Formatting ncbi's databases -- Running blastall -- Downloading pre-formatted databases -- Fastacmd -- Bl2seq -- Performing local blast searches with perl -- Sequence annotation -- Assignments -- 4. Web-based sequence analysis: gene prediction -- Introduction -- Terminology and concepts -- Gene prediction programs -- Genscan -- Running genscan analyses -- Analyzing genscan output -- Genscan analysis with lwp::useragent -- Assignments -- 5. Web-based sequence analysis: hmmer -- Introduction -- Downloading hmmer -- Why use hmmer? -- Running hmmer commands -- Hmmer: a practical example -- Hmmer utilities -- Assignments -- References -- 6. Psi-blast -- Introduction -- Psi-blast and protein analysis -- When is psi-blast better than blastp? -- The design of psi-blast -- Advantages of psi-blast -- Limitations of psi-blast -- Example of a psi-blast search -- Assignments -- B. Part two: applications -- 7. Accessing sequence information using bioperl -- Bioperl installation -- Bioperl modules -- Object oriented programming -- Using bioperl -- The write_seq() function -- Assignments -- Appendix i: installing external modules -- Appendix ii: upgrading bioperl -- Appendix iii: testing for availability of individual modules -- 8. Bio::db::genbank -- Introduction -- Structure of a genbank record -- The bio::db::genbank module -- Assignments -- 9. Accessing genbank data -- Introduction -- Genbank tags -- Extracting tags and their values -- Sample scripts -- Assignments -- 10. Bioperl blast modules -- Introduction -- Blast programs -- Blast2 -- Perl modules for blast2 -- Using bioperl for blast2 -- Standalone blast -- Configuring blastall -- Bio::tools::run::standaloneblast -- Performing blast searches -- Formatting ncbi's databases -- Running blastall -- Running blast with bio::tools::run::standaloneblast -- Assignments -- 11. Parsing blast output -- Generating a raw blast report -- The bio::tools::blast module -- Parsing the hpr blast report -- Specifying a filter function -- Formatting parsing results into a table or html -- Assignments.

Also issued in online version.

Description based on cover image and table of contents, viewed on Jan. 20, 2015.