Bioinformatics Data Representation and IntegrationTable of ContentsWhat is BioinformaticsProtein and SequencesProteins and SequencesBioinformatic ToolsSlide 7Biological DatabasesSlide 9Slide 10Specialized DatabasesPrimary Sequence DatabaseProtein Sequence DatabaseOther DatabasesBlastQuick DiversionSlide 17Blast Functions in DatabasesThe Blast FunctionsParameter DescriptionSlide 21How the whole system WorksHow does it workThe Search ProcedureOutput ResultsThe Databases and WhyBioindexingThe Blast Database and BioindexingTypes of IndexingSlide 30Location (How it is represented)Complexity (Where Clauses ) if no location Datatypes Est sequences being needed to be grouped over consecutive overlapping EST fragmentsLocation DatatypeSimplicity using Location Datatype “Creation and Insertion”Slide 35Slide 36Why location datatype is NeededComplexity without locationsSimplicity using locationsLocation SupportGISTGist ImplementationWhat gist location doesConclusionReferencesBioinformatics Data Representation and IntegrationByNgozi OlelehTable of Contents•Introduction to Bioinformatics•Proteins and Sequences•Bioinformatics Tools•The databases•Blast Functions•Bioindexing•ConclusionWhat is Bioinformatics•Bioinformatics is the use of computers to study and handle biological Information•Bioinformatics can be looked at as an integration of computer science and Biology to help enhance the study of biological data which has been proven to be very extensive•The role of computer science in this Interdisciplinary is to store the data(via databases) for future Analysis via biological tools•This field’s study includes but is not limited to the study of genes, dna sequences and protein structuresProtein and Sequences•Biological proteins are made up of 20 amino acids•Alanine - ala - A •arginine - arg – R •asparagine - asn – N •aspartic acid - asp – D •cysteine - cys – C •glutamine - gln – Q •glutamic acid - glu - E•glycine - gly – G •Histidine - his – H •isoleucine - ile – I •leucine - leu – L •lysine - lys – K •methionine - met – M •phenylalanine - phe – F •proline - pro – P •serine - ser – S •threonine - thr - T •Tryptophan - trp - W •tyrosine - tyr – Y •valine - val – VProteins and Sequences•Combination of these amino acids make up protein structures and sequences•Pdb database contains numerous protein structures that are similar by sequence alignment of fold recognition.•Bioinformatics studies difference and similarities of these protein structures based on sequence similarity •A Sequence is a combination of amino acids.•This sequences can contain biological data, that can be used to denote information about families of proteinsBioinformatic Tools•Mage– Used to display protein singular structures•Rasmol–Used to display protein 3d Structure•LALIGN –For pairwise Sequence Alignment•ClustalW –Used for Multiple Sequence Alignment•Ammp –Molecular Modeling•Sequence Alignment Tools–FASTA –BLAST (will be looked at extensively)Biological Databases•There are over 5000 public biological databases•These databases contain genomic, proteomic and microarray data.•This so called data is made up of sequence of genes or amino acids of proteins•Biological databases have become very useful to scientists. It is important in understanding and explaining a host of biological phenomena from the structure of biomolecules and their interaction, to the whole metabolism of organisms and to understanding the evolution of species.•This knowledge helps facilitate the fight against diseases, assists in the development of medications and in discovering basic relationships amongst species in the history of life.•The biological knowledge is distributed amongst many different general and specialized databases. This sometimes makes it difficult to ensure the consistency of information.• Biological databases cross-reference other databases with accession numbers as one way of linking their related knowledge together.•Bioinformatics databases can be grouped into 2 groups: Generalized databases and Specialized databases•Generalized databases–Primary Sequence Databases (EMBL, Genebank,DDJB)–Protein Sequence Databases(Swiss-prot,UniProt, UniRef)–Carbohydrate Databases (CarbBank)–3d structure Databases (PDB, EBI-MSD,NDB)Specialized Databases•Specialized databases–Specialized Sequence database–Genome databases–Specialized Protein Sequence database–Specialize Structure databases –Microarray databasesMain focus are the Generalized databasesPrimary Sequence Database•Primary sequence databases – EMBL (European Molecular Biology Laboratory nucleotide sequence database at EBI, Hinxton, UK)–GenBank (at National Center for Biotechnology information, NCBI, Bethesda, MD, USA)–DDBJ (DNA Data Bank Japan at CIB , Mishima, Japan)Protein Sequence Database•Protein sequence databases – SWISS-PROT (Swiss Institute of Bioinformatics, SIB, Geneva, CH) –TrEMBL (=Translated EMBL: computer annotated protein sequence database at EBI, UK) –PIR-PSD (PIR-International Protein Sequence Database, annotated protein database by PIR, MIPS and JIPID at NBRF, Georgetown University, USA) –UniProt (Joined data from Swiss-Prot, TrEMBL and PIR) –UniRef (UniProt NREF (Non-redundant REFerence) database at EBI, UK) –IPI (International Protein Index; human, rat and mouse proteome database at EBI, UK)Other Databases•Carbohydrate databases –CarbBank (Former complex carbohydrate structure database) •3D structure databases –PDB (Protein Data Bank cured by RCSB, USA)–EBI-MSD (Macromolecular Structure Database at EBI, UK ) –NDB (Nucleic Acid structure Database at Rutgers State University of New Jersey , USA)BlastBlast is a heuristic algorithm to detect sequencesimilarity and is optimized for speed. It is suitablefor large scale analysisWhat blast does is to match a queried sequence tocertain positions of database sequencesQuick Diversion•Blast Example•Sequence to be queriedTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQ•Sequences producing significant alignments: Score(Bits) E Value• pdb|2FXP|A Chain A, Solution Structure Of The Sars-Coronaviru... 82.4 3e-17 pdb|2BEZ|F