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LaboratoryEuropeanBioinformaticsInstituteSRSSequenceor descriptionsSequenceor descriptionsDNADatabankofJapanNational Center for Biological InformationThe Life Sciences Search Engine(NIH genetic sequence database)
55What Use is All this Sequence Information?•Predict protein structure and function•Predict domain(s) present in the sequence•Predict sub-cellular location•Predict post-translational modifications•Infer evolutionary (phylogenetic) relationshipsAll these tasks require fast, robust, and reliablealignment of sequences
56Sequence Alignment:A Fundamental Concept in Bioinformatics•Aligningsequences of nucleic acids or the encoded proteins (amino acid chains) allows us to infer the properties of a novel gene/sequence by inferencebased on sequence similarity to a previously characterized gene.•This process provides the basis for–structure and function prediction (for even small regions of a protein)–regulatory properties–phylogenetic inferenceFurther reading: David W. Mount. 2001. Bioinformatics. Sequence & Genome Analysis. CSH Press.
57Sequence Alignment:A Fundamental Concept in BioinformaticsBLAST (Basic Local Alignment Search Tool)•One of the fastest and most robust algorithms for searching an entire database for regions of similarities.•Ideal for finding domain similarities and classifying (annotating) a gene based on function.•Not appropriate for inferring evolutionary relationships.Homologous Sequences•Orthologs –genes separated by speciation•Paralogs –genes produced by gene duplication within the same speciesPhylogenetics
58Phylogenetics:Reconstructing evolutionary history and understanding the evolutionaryrelationships amongorganisms.