Databases in Bioinformatics. Molecular Databases. Molecular Databases. NCBI Databases. BINF 630: Bioinformatics Methods
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1 Databases in Bioinformatics BINF 630: Bioinformatics Methods Iosif Vaisman Molecular Databases Molecular Databases Nucleic acid sequences: GenBank, DNA Data Bank of Japan, EMBL Nucleotide Sequence Database Nucleic acid structures: NDB - Nucleic Acid Database Protein sequences: PIR - Protein Information Resource, SWISS-PROT Protein structures: PDB - Protein Data Bank, NRL_3D Physical properties: Biological Macromolecule Crystallization Database, BioMagResBank Molecular images: SWISS-3DIMAGE, Molecules R US NCBI integrated search and retrieval system NCBI Databases nr - All non-redundant GenBank CDS translations+pdb+swissprot+pir month - All new or revised GenBank CDS released in the last 30 days swissprot - the last major release of the SWISS-PROT protein sequence database (no updates) yeast - Yeast (Saccharomyces cerevisiae) protein sequences. E. coli - E. coli genomic CDS translations pdb - Sequences derived from the 3-dimensional structure Brookhaven Protein Data Bank kabat - Kabat's database of sequences of immunological interest
2 Database Database database file record field character a collection of related structured information about entities a collection of records a set of fields a single characteristic of an entity a symbol used in data field Example of a Genbank entry LOCUS VIBHALUXA 3141 bp DNA BCT 15-FEB-1996 DEFINITION V.harveyi luciferase alpha and beta subunit (luxa and luxb) genes, complete cds. ACCESSION M10961 M13494 NID g KEYWORDS luciferase. SOURCE Vibrio harveyi DNA. ORGANISM Vibrio harveyi Eubacteria; Proteobacteria; gamma subdivision; Vibrionaceae; Vibrio. REFERENCE 1 (bases 1 to 1838) AUTHORS Cohn,D.H., Mileham,A.J., Simon,M.I., Nealson,K.H., Rausch,S.K., Bonam,D. and Baldwin,T.O. TITLE Nucleotide sequence of the luxa gene of Vibrio harveyi and the complete amino acid sequence of the alpha subunit of bacterial luciferase JOURNAL J. Biol. Chem. 260 (10), (1985) MEDLINE REFERENCE 2 (bases 1745 to 3141) AUTHORS Johnston,T.C., Thompson,R.B. and Baldwin,T.O. TITLE Nucleotide sequence of the luxb gene of Vibrio harveyi and the complete amino acid sequence of the beta subunit of bacterial luciferase JOURNAL J. Biol. Chem. 261 (11), (1986) MEDLINE Example of a Genbank entry FEATURES Location/Qualifiers gene /gene="luxa" CDS /gene="luxa" /codon_start=1 /product="luciferase alpha subunit" /db_xref="pid:g155175" /transl_table=11 /translation="mkfgnflltyqppelsqtevmkrlvnlgkasegcgfdtvwlleh HFTEFGLLGNPYVAAAHLLGATETLNVGTAAIVLPTAHPVRQAEDVNLLDQMSKGRFR FGICRGLYDKDFRVFGTDMDNSRALMDCWYDLMKEGFNEGYIAADNEHIKFPKIQLNP SAYTQGGAPVYVVAESASTTEWAAERGLPMILSWIINTHEKKAQLDLYNEVATEHGYD VTKIDHCLSYITSVDHDSNRAKDICRNFLGHWYDSYVNATKIFDDSDQTKGYDFNKGQ WRDFVLKGHKDTNRRIDYSYEINPVGTPEECIAIIQQDIDATGIDNICCGFEANGSEE EIIASMKLFQSDVMPYLKEKQ" BASE COUNT 883 a 665 c 741 g 852 t ORIGIN 1 bp upstream of EcoRI site. 1 gaattcacca tgacgacggg caaaaatagt ttgtgcactg tttatcactg gctgcagacc 61 aagggcacac aaaacattgg cttgattgcg gcaagtctct cagctcgtgt cgcctatgaa 121 gttatctctg atctggagct gtcttttctg attactgcgg ttggtgtggt gaacttgcgt 181 gacacactag aaaaagcgct tggttttgat tacctcagtt tgcctatcga tgagctacca... Example of a Pubmed entry PMID OWN - NLM STAT- MEDLINE DA DCOM IS (Electronic) IS (Linking) DP Aug 15 TI - New method for protein secondary structure assignment based on a simple topological descriptor. PG AB - A simple, five-element descriptor, derived from the Delaunay tessellation of a protein structure in a single point per residue representation, can be assigned to each residue in the protein. The descriptor characterizes main-chain topology and connectivity in the neighborhood of the residue and does not explicitly depend on putative hydrogen bonds or any geometric parameter, including bond length, angles, and areas. Rules based on this descriptor can be used for accurate, robust, and computationally efficient secondary structure assignment that correlates well with the existing methods. AD - Laboratory for Structural Bioinformatics, School of Computational Sciences, George Mason University, Manassas, Virginia 20110, USA. FAU - Taylor, Todd AU - Taylor T FAU - Rivera, Margarita AU - Rivera M FAU - Wilson, Glenda AU - Wilson G FAU - Vaisman, Iosif I AU - Vaisman II LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States Example of a Pubmed entry TA - Proteins JT - Proteins JID RN - 0 (Proteins) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Biophysical Phenomena MH - Biophysics MH - Computational Biology/*methods MH - Computer Simulation MH - Hydrogen Bonding MH - Models, Chemical MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proteins/chemistry MH - Proteomics/*methods MH - Sensitivity and Specificity MH - Software MH - Structural Homology, Protein EDAT- 2005/05/12 09:00 MHDA- 2006/05/23 09:00 CRDT- 2005/05/12 09:00
3 Database Organization Database Management System (DBMS) Four major components of DBMS: Data * Hardware * Software * Users Data Model Relational Database Model A named logical unit (record type, data item) Relationships among logical units Relationships among logical units one to one one to many many to one Database administration Derivative databases Redundancy eliminated Inconsistency avoided Data shared Standards enforced Security applied Integrity maintained Requirements balanced Lu, 2010
4 Data integration Data Warehouse Operational data Data fusion Large-scale, complex data sets are shown as a network in which the nodes represent variables of biological interest, such as DNA variation, RNA variation, protein levels, protein states, metabolite levels and diseaseassociated traits, and the edges between these nodes represent causal relationships between the variables. Data cleansing Metadata InterPro Database Infrastructure organization Cloud computing Types of computational environments
5 Types of computational environments
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Contents Computational Methods for Protein Structure Prediction and Fold Recognition........................... 1 I. Cymerman, M. Feder, M. PawŁowski, M.A. Kurowski, J.M. Bujnicki 1 Primary Structure Analysis...................