Dedan Githae Email: d.githae@cgiar.org BecA-ILRI Hub; Nairobi, Kenya 16 May, 2014 ONLINE BIOINFORMATICS RESOURCES Introduction to Molecular Biology and Bioinformatics (IMBB) 2014
The larger picture.. Lower cost, Improved efficiency and modern technology: The sequencers, computers, and rate at which data is being produced have all increased in speed - huge amounts of biological data produced at a FASTER rate than interpreted. Storage and Exchange of data: Need to improve database design, develop better software for database access / manipulation, harmonize data-entry procedures to compensate for the varied computer procedures and systems used in different laboratories Computing power, access to information (data) and right software (tools) has enabled scientists increase rate at answering research questions and new discoveries
Online Bioinformatics resources INFORMATION Journals / publications, biological research data. TOOLS Programs to analyse data
Information Journal Website: Almost every major journal has a web access to abstracts is usually free, even when the content is subscription. E-journals: Some electronic journals are online-only journals; some are online versions of printed journals, and some consist of the online equivalent of a printed journal, but with additional online-only (sometimes video and interactive media) material.
Information Servers (eg NCBI Pubmed; Google scholar; SCOPUS) A search engine to search references and abstracts on life sciences and biomedical topics in multiple databases
Sequence Databases Primary Databases: International Nucleotide Sequence Database Collaboration comprises of GenBank (USA), European Nucleotide Archive (Europe) and DNA DataBase of Japan. http://www.ncbi.nlm.nih.gov They cooperate to make all publicly available sequences available. http://www.ebi.ac.uk/ena/
Sequence Databases Secondary Databases UniProt: It is a database of protein sequence and functional information. Information about the biological function of proteins derived from the research literature Available under Uniprot SWISS PROT: Manually annotated and reviewed TrEMBL: Automatically annotated and not reviewed. Uniprot: www.uniprot.org
Other Databases Multigenome: ensembl: genome databases for vertebrates and other eukaryotic species, Genome specific databases: eg Wormbase; Saccharomyces database; Vectorbase; Flu DB; Zebrafish Model Organisms, Flybase etc. NB: You can also access to these genomes from the public databases Biochemical pathway databases: Biological activities are orchestrated by various molecules These include KEGG; ExPASY; MetaCyc; BioPath Gene expression Data: DNA Microarrays: array of probe molecules that can bind specific DNA / mrna. Fluorolabelling enables viewing level of expression of genes; eg NCBI Geo (Gene experssion omnibus) Expression Atlas (EBI) 2D PAGE: allows quantitative study of protein concentration in www.yeastgenome.org/ the cell. Eg SWISS-2D PAGE www.fudb.org www.zfin.org www.wormbase.org/ http://vectorbase.org/ http://www.metacyc.org/ KEGG: http://www.genome.jp http://web.expasy.org/pathways/ http://www.molecular-networks.com/databases/biopath http://www.ncbi.nlm.nih.gov/geo/ http://www.ebi.ac.uk/gxa http://world-2dpage.expasy.org/swiss-2dpage/
Protein Structure Databases Protein Databank (PDB) (experimentally validated) Secondary & Others: ModBase: A database of annotated comparative protein structure models Modelled proteins) SCOP: Structural classification of Proteins Depending on α ; β ; α+β ; membrane & cell surface proteins; small proteins; coiled coil proteins, etc CATH: hierarchical domain classification of protein structures in the Protein Data Bank (Class Architecture Topology Homologous superfamilies) www.pdb.org https://modbase.compbio.ucsf.edu/modweb/
Softwares / Tools Sources of (informative) tools: Journals eg Bioinformatics, Nucleic Acids Research, Journal of Molecular Biology, Protein science publish papers on cutting edge developments and innovations in computational biology methods Most biological databases have software resource listings- eg Sequence searching, visualisation resources (genome / alignment / genome level). Web servers: Simple web implementation of the softwares. Clear inputs, outputs, parameters, graphical data representation and downloadable results.
Basic tasks Task Objective Tool Sequence similarity Sequence alignment Gene finding DNA Translation Local pairwise alignment Global pairwise alignment Identify homologous sequences to gain information Identify conserved regions, domains, motifs Identify coding regions in gdna sequences Convert DNA Sequence to protein Detect short regions of homology in longer sequences Find the best full length alignment in 2 sequences BLAST; SSEARCH; FASTA, ENA search CLUSTAL; Muscle; GENSCAN; ORFinder; GRAIL Various servers and tools eg ExPasy, Transeq, EBI, and ORFinders BLAST; FASTA ALIGN http://web.expasy.org/translate/
http://www.ebi.ac.uk/tools
http://www.ebi.ac.uk/tools
Protein Domains A protein domain is a conserved part of a given protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. Databases include: SMART; PROSITE; NCBI; CATH GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE (GAR-SYN) FROM E. COLI. http://prosite.expasy.org/ http://smart.embl-heidelberg.de/
Motifs A motif is a locally, conserved region / short sequence pattern shared by set of sequence; (Multiple sequence analysis) Thus can be indicative of function / structural similarities. Can be displayed via Sequence logos, or as patterns of amino acids. Patterns of amino acids [PROSITE]: For example N-glycosylation site motif takes the form: N{P}[ST]{P} To mean: Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro
DSSP: Wolfgang Kabsch and Chris Sander EXPASY: seconadary structure prediction JPRED 3: from university of Dundee PDB: DSSP prediction
Honorable mention About PredictProtein PredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intraresidue contacts, protein-protein and protein-dna binding sites, sub-cellular localization, domain boundaries, beta-barrels, cysteine bonds, metal binding sites and disulphide bridges. Listed below is a comprehensive list of methods and databases currently incorporated into the server.
Integrated Methods Method Name Description Reference Web Server Download PROFphd Prediction of secondary structure and solvent accessibility - - ftp://rostlab.org/profphd PHDhtm Prediction of transmembrane helices - - ftp://rostlab.org/profphd PROFtmb Prediction of transmembrane beta-barrels - - ftp://rostlab.org/proftmb NORSp Predictor of non-regular secondary structure - - ftp://rostlab.org/norsp NCOILS Calculates the probability that the sequence will adopt a coiled-coil conformation - - - SEG Identifies low complexity regions - - - DISULFIND Prediction of disulfide bridges - - ftp://rostlab.org/profbval PROFBval Prediction of residue mobility - - ftp://rostlab.org/profbval NorsNet Prediction protein disordered sites - - ftp://rostlab.org/norsnet UCON Contact based prediction of disordered sites - - METADISORDER Consensus based prediction of protein disorder - - ISIS Prediction of protein-protein interaction sites - - LocTree2 Prediction of sub-cellular localization for all domains of life - - - MetaStudent Prediction of GO terms for Molecular Function and Biological Process - - ftp://rostlab.org/metastudent SNAP2 Prediction of functional changes due to single nucleotide polymorphism - - - ConSurf Prediction of functional changes due to single nucleotide polymorphism - - - Supporting Databases Database Name Description Reference Download UniRef Used for sequence homology searches by PSI-BLAST abstract http://www.uniprot.org/help/uniref PDB The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwpdb, the RCSB PDB curates and annotates PDB data according to agreed upon standards. abstract http://www.rcsb.org/pdb/download/download.do Pfam A collection of protein families abstract ftp://ftp.sanger.ac.uk/pub/databases/pfam/releases/ PROSITE Database of biologically significant sites, patterns and profiles abstract ftp://ftp.expasy.org/databases/prosite/
In a Nutshell There is vast amount of available out there. There is a vast number of tools out there.. Select best that is applicable for your project..
Thank you Dedan Githae Bioinformatician BecA-ILRI Hub d.githae@cgiar.org Online Bioinformatics resources http://hub.africabiosciences.org