Biology asks six kinds of questions

Transcription

1 BIOINFO LANGUAGE: SEQUENCE FORMATS/CONVERSION ATGATGTCGATTTCGGCTTTTCCTTTAAGTGTA GGAATTGCGTTTGCTACGTTGAGTTACTTTTTA CTAAAGGTAAATGGATGTATTTATATGTGTATG TGTTTGGAAATAT Raphael D. Isokpehi, PhD, Cynthia Jeffries, Nyasha Chambwe, Zandra Cole, Hari H.P. Cohly Department t of Biology Jackson State University Jackson MS raphael.isokpehi@jsums.edu Bioinformatics for High School and College Instructors 2008 National Science Foundation EPSCoR June 4, 2008

2 Biology asks six kinds of questions How is it built? Structurest How does it work? Mechanisms What goes wrong? Pathologies How is it fixed? Repairs How did d it begin? Origins What is it for? Functions or Purposes - Joel E. Cohen, PLoS Biology Dec. 2004

3 Hierarchical Organization of the Biological i l World Cellular Organismal Population Level Level Tissue Population Level Atoms Molecule Macromolecule Organelle Organ Species Organ System Community Cell Organism Ecosystem

4 GENOME BASICS (1) SEQUENCE Order of letters that represent acids that encode genetic information Nucleotide Sequence From Nucleic Acids: DNA, RNA Combination of nucleotides (Sugar, nitrogenous base and phosphate group) Adenylic acid (A), Guanylic acid (G) Cytidylic acid (C), Uridylic acid (U), Thymidylic acid (T) Amino Acid Sequence 20 amino acids Codons (Three nucleotides code for one amino acid)

5 GENOME BASICS (2) Structure of DNA

6 GENETIC CODE

7 GENOME BASICS (3) DNA Structure Bioinformatician s View BY EWAN BIRNEY BY EWAN BIRNEY Head of the Ensembl project at the European Bioinformatics Institute, UK

8 GENOME BASICS (4) Nucleotide and Amino Acid Sequences >PFA0025c ATGATGTCGATTTCGGCTTTTCCTTTAAGTGTAGGAATTGCGT TTGCTACGTTGAGTTACTTTTTACTAAAGGTAAATGGATGTAT TTATATGTGTATGTGTTTGGAAATAT (Length: 112 base pairs (bp)) >PFA0025c MMSISAFPLSVGIAFATLSYFLLKVNGCIYMCMCLEI (Length: 37 amino acids (aa))

9 CENTRAL DOGMA OF MOLECULAR BIOLOGY DNA mrna ATGATGTCGATTTCGGCTTTTCCTTTAAGTGTA GGAATTGCGTTTGCTACGTTGAGTTACTTTTTA CTAAAGGTAAATGGATGTATTTATATGTGTATG TGTTTGGAAATAT AUGAUGUCGAUUUCGGCUUUUCCUUUAAGUGUA GGAAUUGCGUUUGCUACGUUGAGUUACUUUUUA CUAAAGGUAAAUGGAUGUAUUUAUAUGUGUAUG UGUUUGGAAAUAU Protein MMSISAFPLSVGIAFATLSYFLLKVNGCIYMCM CLEI

10 PROGRESS IN NUCLEOTIDE SEQUENCING PCR Machine ABI PRISM 310 DNA Sequencer

11 PROGRESS IN COMPUTER HARDWARE AND SOFTWARE 1981 IBM PC

12 GENOME SEQUENCING PROJECT Library Construction Genome Sequencing Genome Assembly Gap Closure Gene Prediction Gene Annotation Genome Analysis (e.g. Comparative and Integrative)

13 Growth of INSDC DNA sequence database has exceeded d 100 gigabases Status: April 15, loci, bases, from reported sequences Status: April 15, loci, bases, from reported sequences

14 FOUNDATIONS AND APPLICATIONS OF BIOINFORMATICS Algorithms Community Data acquisition Graphics, visualisation databases Data deconvolution Signal processing Genome mapping & comparison Structure determination Computer architectures Molecular modeling & simulation Artificial intelligence Structure-based drug design Database management Structure alignment & comparison Statistics Laboratory data Structure prediction Simulation management Sequence alignment Information theory Image processing Robotics Molecular evolution Database query tools Gene identification Software engineering Computational Foundations Data Sources Bioinformatics Application

15 GENOME PROJECTS ORGANISM Haemophilus influenzae KW20 Methanococcus jannaschii DSM 2661 Helicobacter pylori Escherichia coli K12 Saccharomyces cerevisiae S288C Mycobacterium tuberculosis H37Rv Caenorhabditis elegans Arabidopsis thaliana Homo sapiens Shewanella oneidensis MR-1 Plasmodium falciparum 3D7 Caenorhabditis briggsae Cryptosporidium parvum Tetraodon nigroviridis Natronomonas pharaonis Clostridium botulinum strain Hall A Treponema pallidum YEAR SEQUENCING CENTER TIGR TIGR TIGR University of Wisconsin International Collaboration Sanger WashU and Sanger International Collaboration International ti lcollaboration TIGR International Collaboration WashU UCSF, Univ. of Minnesota Genoscope, Broad Institute Max-Plank Institute Wellcome Trust Baylor College of Medicine

16 Human Genome Sequencing Project International Consortium 24 Chromosomes 3,000+ Mb At least 30, genes Web access:

17 January 2007: 41 Archaea; 478 Bacteria; 49 Eukaryota January 2008: 53 Archaea; 662 Bacteria; 94 Eukaryota

18 POST-GENOME PROJECTS Microarray Proteomics SNP Metabolomics

19 ROUTINE BIOINFORMATICS ANALYSIS SEARCHING DATABASES How is the sequence I have similar to other sequences in a database? Software: BLAST (Basic Local Alignment Search Tool) SECTION OF BLAST OUTPUT Query= queryseq (337 letters) Database: Amino acid sequences for annotated Plasmodium falciparum genes 5279 sequences; 4,004,627 total letters Searching...done Score E Sequences producing significant alignments: (bits) Value [HSPs] P. falciparum 3D7 Annotated PF14_ [HSPs] P. falciparum 3D7 Annotated PF13_

20 ROUTINE BIOINFORMATICS ANALYSIS ALIGNING SEQUENCES What is the sequence identity between two sequences? Software: CLUSTALW AF MKIANYLSAINLFVVLLMSFKNAHDTSLINTNKCAHNMVGNNRILGNIPSDNTEDSSNQV AF MKIANYLSAINLFVVLLMSFKNAHDTSLINTNKCAHNMVGNNRILGNIPSDNTEDSSNQV ************************************************************ AF EGNADSNEVTSEEAKNTSNQGNGENANQAGTPAEPAKADATQNAAAQPDNTNGTGSKTTD AF EGNADSNEVTSEEAKNTSNQANGETANQAGTPAEPAKADATQNSPAQPDNTNGTESKTTG ******************** ***.******************. ********* **** AF ANVTLLSSEEDDEEEDDDTEYEEGNCEVNNGGCGPNLKCEKMPNGAIKCSCPSGFKLQGT AF EKATLLSSEEDDEEEDDDDELEDGDCSVDNGGCGENLICEKMENGRIKCSCPSGYKLHGT *************** * *.* * * ***** ** **** ** ********.**.** AF DCIALFSADSVNYSFCGIIMVAIAIIALLY AF DCIALLSADSVNYSFCGIIMVAIAIIALLY ***** ************************ *=identity; gap=difference; period=similarity

21 Comparative Analysis Similarities and Differences Genome and Post-genome datasets: Pathogenic genome vs. Non-Pathogenic genome Merozoite Stage vs. Gametocyte Stage Chromosome 1 vs. Chromosome 2 Pairwise Comparison of members of gene families Methodologies: Microarray vs. EST Microarray vs. Proteomics Microarray vs. Differential Display Glimmer vs. Phat (Prediction of genes at telomeres)

22 Acquisition of Sequences Sequence Processing Identification of Orthologous Genes in Two Genomes using Reciprocal Best Match Database Formatting BLAST Searches Satisfy E-value? Yes Reciprocal Match? Yes No No Non-significant Matches Sequences without Orthologues Putative Orthologues Hide WA and Isokpehi RD (2004) Positive selection scanning of parasite DNA sequences. Methods in Molecular Biology, Vol. 271: Parasite Genomics Protocols.

23 Integrative Analysis Consolidate Diverse Data Genome and Post-genome datasets: Genomic, EST, Microarray, Proteomic, Gene Ontology Phylogenetic Relationship, Pfam Domain Methodologies: Microarray, Differential Display, Differential Slot Genomic, EST, Microarray, Proteomic and Gene Ontology cdna microarray, Oligo microarray, Affymetrix Chips Outputs Appraisal of datasets Insights into biology of organism Improve quality of datasets

24 POST-GENOME PROJECTS Microarray Proteomics SNP Metabolomics

25 Sequence Formats Sequence formats - the way in which the amino acid or DNA sequence is recorded in a computer file Different programs recognized different formats Tools are available to convert from one sequence format to another

26 Phylogeny Is the evolution of a genetically related group of organisms. A study of relationships between collection of "things" (genes, proteins, organs..) that are derived from a common ancestor.

27 Sequence Formats ALN/ClustalW format AMPS Block file format ClustalW Codata EMBL GCG/MSF GDE Genebank Fasta(Pearson) NBRF/PIR PDB format Pfam/Stockholm format Phylip Raw RSF UniProtKB/Swiss-Prot

28 ALN/ClustalW format: Originated in ClustalW alignment program File starts with the word CLUSTAL Alignment written in blocks of 60 residues Every block shows sequence names At end of block count of total number of residues is shown

29 Type of clustal program used Version of clustal l Sequence name Residues or nucleotides in column are identical all sequences are in alignment Semi-conserved substitutions observed Conserved substitutions observed

30 first line starts with the text ENTRY Codata Format "SEQUENCE" line specifies the beginning of the sequence lines (starting on the next line) no sequence is assumed to appear in the entry if the "SEQUENCE" line is missing. end of a sequence is delineated by "///".

31 Header-tells the description of the sequence Example of FASTA Format >FOSB_MOUSE Protein fosb. 338 bp MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS GGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELT DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRD LPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLFTHSEVQVLGDPFPVVSPSY TSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLAL sequence ** FASTA files ignore spaces or other gaps symbols in a sequence They ** FASTA files ignore spaces or other gaps symbols in a sequence. They are preceded by a line starting with a > symbol.

32 Multiple Sequence Alignment of Human and Rodent Plasmodia AQP

33 A Traditional GenBank Record LOCUS AY bp mrna linear PLN 04-MAY-2004 DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mrna, complete cds. ACCESSION AY VERSION AY GI: KEYWORDS. SOURCE Malus x domestica (cultivated apple) ORGANISM Malus x domestica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus. REFERENCE 1 (bases 1 to 1931) AUTHORS Pechous,S.W. and Whitaker,B.D. TITLE Cloning and functional expression of an (E,E)-alpha-farnesene synthase cdna from peel tissue of apple fruit JOURNAL Planta 219, (2004) REFERENCE 2 (bases 1 to 1931) AUTHORS Pechous,S.W. and Whitaker,B.D. TITLE Direct Submission JOURNAL Submitted (18-NOV-2002) PSI-Produce Quality and Safety Lab, USDA-ARS, Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD 20705, USA REFERENCE 3 (bases 1 to 1931) AUTHORS Pechous,S.W. and Whitaker,B.D. TITLE Direct Submission JOURNAL Submitted (25-JUN-2003) PSI-Produce Quality and Safety Lab, USDA-ARS, Baltimore Ave. Bldg. 002, Rm. 205, Beltsville, MD 20705, USA REMARK Sequence update by submitter COMMENT On Jun 26, 2003 this sequence version replaced gi: FEATURES Location/Qualifiers source /organism="malus x domestica" /mol_type="mrna" /cultivar="'law Rome'" /db _ xref="taxon:3750" /tissue_type="peel" gene /gene="afs1" CDS /gene="afs1" /note="terpene synthase" /codon_start=1 /product="(e,e)-alpha-farnesene synthase" /protein_id="aao " /db_xref="gi: " /translation="mefrvhlqadneqkifqnqmkpepeasylinqrrsanykpniwk NDFLDQSLISKYDGDEYRKLSEKLIEEVKIYISAETMDLVAKLELIDSVRKLGLANLF EKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQHGYKVSQDIFGRFMDEKGTLE NHHFAHLKGMLELFEASNLGFEGEDILDEAKASLTLALRDSGHICYPDSNLSRDVVHS LELPSHRRVQWFDVKWQINAYEKDICRVNATLLELAKLNFNVVQAQLQKNLREASRWW ANLGIADNLKFARDRLVECFACAVGVAFEPEHSSFRICLTKVINLVLIIDDVYDIYGS EEELKHFTNAVDRWDSRETEQLPECMKMCFQVLYNTTCEIAREIEEENGWNQVLPQLT KVWADFCKALLVEAEWYNKSHIPTLEEYLRNGCISSSVSVLLVHSFFSITHEGTKEMA DFLHKNEDLLYNISLIVRLNNDLGTSAAEQERGDSPSSIVCYMREVNASEETARKNIK GMIDNAWKKVNGKCFTTNQVPFLSSFMNNATNMARVAHSLYKDGDGFGDQEKGPRTHI LSLLFQPLVN" ORIGIN 1 ttcttgtatc ccaaacatct cgagcttctt gtacaccaaa ttaggtattc actatggaat 61 tcagagttca cttgcaagct gataatgagc agaaaatttt tcaaaaccag atgaaacccg 121 aacctgaagc ctcttacttg attaatcaaa gacggtctgc aaattacaag ccaaatattt 181 ggaagaacga tttcctagat caatctctta tcagcaaata cgatggagat gagtatcgga 241 agctgtctga gaagttaata gaagaagtta agatttatat atctgctgaa acaatggatt 1801 aataaatagc agcaaaagtt tgcggttcag ttcgtcatgg ataaattaat ctttacagtt 1861 tgtaacgttg ttgccaaaga ttatgaataa aaagttgtag tttgtcgttt aaaaaaaaaa 1921 aaaaaaaaaa a // Header Feature Table Sequence The Flatfile Format

34 Readseq - biosequence conversion tool Option to specify output format Gives the option to upload sequence file or to cut and paste sequences for submission

35 STANDARD VOCABULARIES FOR SEQUENCE FORMATS XML: exensible Markup Languange GFF: an Exchange Format for Feature Description SO: Sequence Ontology,

36 GFF XML FORMAT

37 SEQUENCE ONTOLOGY

38 NIH Grant No. 1G12RR13459 ACKNOWLEDGEMENTS NCRR-RCMI RCMI Center for Environmental Health at Jackson State University Interdisciplinary Undergraduate Training in Biological and Mathematical Sciences (DMS ) Mississippi i i insf-epscor "Innovations through h Computational ti Sciences" Award (EPS ) Office of Research Development and Federal Relations (Jackson State University) A research thrust of the Mississippi NSF-EPSCoR