Basics on bioinformatics Lecture 2. Nunzio D Agostino

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1 Basics on bioinformatics Lecture 2 Nunzio D Agostino

2 Database or databank? Initially o Databank(UK) o Database(USA) Solution The abbreviation db 2

3 Entity-Relationship(ER) modeling Notation uses three main constructs: o Data entities Represents a set or collection of objects in the real world that share the same properties. Person, place, object, event or concept about which data is to be maintained. o Attributes Named property or characteristic of an entity o Relationships Association between the instances of one or more entity types Relationships can be classified as either one to one 11 one to many 1N many to many NN Connectivity 3

4 Cardinality 1 : 1 1 : N N: M 4

5 ER example 5

6 database: basic structure Gi Accession Length Cultivar Dev.stag Tissue sequence CD Turning stage of fruit ripening Pericarp GTACTCCTAAAC BI TA days old callus CCACAACCACA AJ West Virginia dayspost anthesis fruit CAAATTTA.. Databases are composed of tables of data. Tables hold logically related sets of data. A table is essentially the same thing as a spreadsheet: a set of rows and columns 6

7 database: basic structure Gi Accession Length Cultivar Dev.stag Tissue sequence CD Turning stage of fruit ripening Pericarp GTACTCCTAAAC BI TA days old callus CCACAACCACA AJ West Virginia dayspost anthesis fruit CAAATTTA.. Each table has several records or entries : a record stores all the information for a given individual Records are therowsof a data table 7

8 database: basic structure Gi Accession Length Cultivar Dev.stag Tissue sequence CD Turning stage of fruit ripening Pericarp GTACTCCTAAAC BI TA days old callus CCACAACCACA AJ West Virginia dayspost anthesis fruit CAAATTTA.. Each record has several fields: A field is an individual piece of data, a single attribute of the record. Fields are thecolumnsof a data table 8

9 database: basic structure Gi Accession Length Cultivar Dev.stag Tissue sequence CD Turning stage of fruit ripening Pericarp GTACTCCTAAAC BI TA days old callus CCACAACCACA AJ West Virginia dayspost anthesis fruit CAAATTTA.. Each record (row) has a unique identifier, the primary key. the primary key serves to identify the data stored in this record across all the tables in the database. Databases are manipulated with a language called SQL (Structured Query Language). It s a baby English type of language: uses real words,butrigidintermsoftheorderandplacement. Various database software: Oracle, MS Access, MySQL, etc. 9

10 Why biological databases? omake biological data available to scientists Consolidation of data(gather data from different sources) Provide access to large dataset that cannot be published explicitly(genome, ) omake biological data available in computer-readable format Make data accessible for automated analysis 10

11 Biological db o Vary in size, quality, coverage, level of interest o Many of the major ones covered in the annual Database Issue of Nucleic Acids Research

12 Biological db 12

13 Biological db 13

14 What makes a good db? o comprehensiveness o accuracy o is up-to-date o good interface o batch search/download o API (web services, DAS, etc.) 14

15 must have item when using db o Remember the server, the database, and the program version used o Write down sequence identification numbers o Databases are not like good wine (use up-to-date builds) o Use local installs when it becomes necessary 15

16 Primary and derived data Primary databases: Databases consisting of data derived experimentally such as nucleotide sequences and three dimensional structures. Secondary databases: Those data that are derived from the analysis or treatment of primary data 16

17 Nucleotide sequence databases GenBank The 3 databases are synchronized on a daily basis, and the accession numbers are consistent. There are no legal restriction in the usage of these databases. However, there are some patented sequences in the database 17

18 GenBank sample record LOCUS AF bp DNA linear BCT 19-AUG-1999 DEFINITION Pseudomonas fluorescens ECF sigma factor SigX (sigx) gene, complete cds. ACCESSION AF VERSION AF GI: KEYWORDS. SOURCE Pseudomonas fluorescens. ORGANISM Pseudomonas fluorescens Bacteria; Proteobacteria; gamma subdivision; Pseudomonadaceae; Pseudomonas. REFERENCE 1 (bases 1 to 591) AUTHORS Brinkman,F.S., Schoofs,G., Hancock,R.E. and De Mot,R. TITLE Influence of a putative ECF sigma factor on expression of the major outer membrane protein, OprF, in Pseudomonas aeruginosa and Pseudomonas fluorescens JOURNAL J. Bacteriol. 181 (16), (1999) MEDLINE PUBMED REFERENCE 2 (bases 1 to 591) AUTHORS De Mot,R. TITLE Direct Submission JOURNAL Submitted (04-DEC-1998) F.A. Janssens Laboratory of Genetics, Applied Plant Sciences, K. Mercierlaan 92, Heverlee B-3001, Belgium FEATURES Location/Qualifiers source /organism="pseudomonas fluorescens" /strain="m114" /db_xref="taxon:294" gene /gene="sigx" CDS /gene="sigx" /codon_start=1 /transl_table=11 /product="ecf sigma factor SigX" /protein_id="aad " /db_xref="gi: " /translation="mnkaqtlstrydprelsdeelvarshtelfhvtrayeelmrryq RTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNLEGKSKFKTWLYSITYNECITQYR KERRKRRLMDALSLDPLEEASEEKALQPEEKGGLDRWLVYVNPIDRGILVLRFVAELE FQEIADIMHMGLSATKMRYKRALDKLREKFAGETET" BASE COUNT 157 a 133 c 170 g 131 t ORIGIN 1 atgaataaag cccaaacgct atccacgcgc tacgaccccc gcgagctctc tgatgaggag 61 ttggtcgcgc gctcgcatac cgagcttttt cacgtaacgc gcgcctatga agaactgatg 121 cggcgttacc agcgaacatt atttaacgtt tgtgcgagat atcttgggaa cgatcgcgac 181 gcagacgatg tctgtcagga agtcatgttg aaggtgctgt atggcctgaa gaacctcgag 241 gggaaatcga agttcaaaac gtggctctac agcatcacgt acaacgaatg tattacgcag 301 tatcggaagg aacggcgaaa gcgtcgcttg atggacgcat tgagtcttga ccccctcgag 361 gaagcgtccg aagaaaaggc gcttcaaccc gaggagaagg gcgggcttga tcgctggctg 421 gtgtatgtga acccgattga ccgtggaatt ctggtgcttc gatttgtcgc agagctggaa 481 tttcaggaga tcgcagacat catgcacatg ggtttgagtg cgacaaaaat gcgttacaaa 541 cgtgctctag ataaattgcg tgagaaattt gcaggcgaga ctgaaactta g header features sequence title taxonomy citation 18

19 Protein sequence database The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. UniprotKB Knowledgebase is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. Swiss-Prot, which is manually annotated and reviewed. TrEMBL, which is automatically annotated and is not reviewed. The UniProtReference Clusters (UniRef), which is used to speed up sequence similarity searches. 19

20 UniProt entry 20

21 Protein data bank The PDB archive contains information about experimentally determined structures of proteins, nucleic acids, and complex assemblies.(xray, NMR, Computationally predicted) Mission: maintain a single archive of macromolecular structural data that is freely and openly available to the global community Number of Structures Available 21

22 PDB entry 22

23 Protein structure levels 23

24 The gene Ontology (GO) GO goals The GO Website 24

25 The gene Ontology (GO) GO is divided in 3 domain (levels of annotation): omolecular function - basic activities of a gene product at the molecular level o Biological process - set of molecular events with a defined beginning and an end o Cellular component - the parts of a cell or its extracellular environment 25

26 GO structure The structure of GO can be described in terms of direct acyclic graph (DAG), where each GO term is a node, and the relationships between the terms are arcs between the nodes nucleus chromosome mitochondrion part_of Is_a part_of Nuclear chromosome mitochondrial chromosome GO currently has 2 relationship types: Is_a An is_achild of a parent means that the child is a complete type of its parent, but can be discriminated in some way from other children of the parent. Part_of A part_ofchild of a parent means that the child is always a constituent of the parent that in combination with other constituents of the parent make up the parent. 26

27 Searching for papers

28 Querying GenBank Search from the Entrezmain page the gene whose accession number is BC o How many results we get in the Gene db? o What is the official name of the gene? Other possible names? o On which DNA strand is it located? o How many variants of splicing it has? o Which disease is the gene associated to? o Is it involved in the apoptosis process? o How long is the coding sequence of the first variant of slicing? 28

29 Querying GenBank NG_

30 What kind of molecule is it? Genomic DNA Querying GenBank 30

31 Querying GenBank Where is locate the promoter of the gene HBB? Upstream the nucleotide

32 Querying GenBank Indicate the number of exons= Indicate the length of the second exon= Indicate the number of introns = Indicate the length of the first intron= = 223 nts = 132 nts 32

33 Querying GenBank Indicate the location of the 5 'UTR = Indicate the length of the 5 'UTR = Indicate the location of the 3 'UTR = Indicate the length of the 3 'UTR = = 50 nts = 132 nts 33

34 Querying GenBank Indicate the nucleotide positions of the start codon = 70595,70596,

35 Querying GenBank Download in FASTA format the sequence of the HBB gene 35

36 Querying GenBank

37 Querying GenBank 37

38 Querying GenBank >gi : Homo sapiens beta globin region and hemoglobin, beta (HBB); and hemoglobin, delta (HBD); and hemoglobin, epsilon 1 (HBE1); and hemoglobin, gamma A (HBG1); and hemoglobin, gamma G (HBG2), RefSeqGene on chromosome 11 ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGA GGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGC AGGTTGGTATCAAGGTTACAAGACAGGTTTAAGGAGACCAATAGAAACTGGGCATGTGGAGACAGAGAAG ACTCTTGGGTTTCTGATAGGCACTGACTCTCTCTGCCTATTGGTCTATTTTCCCACCCTTAGGCTGCTGG TGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATGCTGTTATGGG CAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGAC AACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACT TCAGGGTGAGTCTATGGGACGCTTGATGTTTTCTTTCCCCTTCTTTTCTATGGTTAAGTTCATGTCATAG GAAGGGGATAAGTAACAGGGTACAGTTTAGAATGGGAAACAGACGAATGATTGCATCAGTGTGGAAGTCT CAGGATCGTTTTAGTTTCTTTTATTTGCTGTTCATAACAATTGTTTTCTTTTGTTTAATTCTTGCTTTCT TTTTTTTTCTTCTCCGCAATTTTTACTATTATACTTAATGCCTTAACATTGTGTATAACAAAAGGAAATA TCTCTGAGATACATTAAGTAACTTAAAAAAAAACTTTACACAGTCTGCCTAGTACATTACTATTTGGAAT ATATGTGTGCTTATTTGCATATTCATAATCTCCCTACTTTATTTTCTTTTATTTTTAATTGATACATAAT CATTATACATATTTATGGGTTAAAGTGTAATGTTTTAATATGTGTACACATATTGACCAAATCAGGGTAA TTTTGCATTTGTAATTTTAAAAAATGCTTTCTTCTTTTAATATACTTTTTTGTTTATCTTATTTCTAATA CTTTCCCTAATCTCTTTCTTTCAGGGCAATAATGATACAATGTATCATGCCTCTTTGCACCATTCTAAAG AATAACAGTGATAATTTCTGGGTTAAGGCAATAGCAATATCTCTGCATATAAATATTTCTGCATATAAAT TGTAACTGATGTAAGAGGTTTCATATTGCTAATAGCAGCTACAATCCAGCTACCATTCTGCTTTTATTTT ATGGTTGGGATAAGGCTGGATTATTCTGAGTCCAAGCTAGGCCCTTTTGCTAATCATGTTCATACCTCTT ATCTTCCTCCCACAGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCA CCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCA CTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACT GGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC 38

39 Querying GenBank 39

40 Querying GenBank: link to geneid 40

41 Querying PUBMED How many articles did Nunzio D Agostino publish? 41

42 Querying PUBMED How many articles did Nunzio D Agostino publish? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] 42

43 Querying PUBMED How many articles did Nunzio D Agostino publish? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] How manyof theseare reletedto EST? 43

44 Querying PUBMED How many articles did Nunzio D Agostino publish? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] How manyof theseare reletedto EST? D'Agostino, Nunzio[Full Author Name] AND EST [Title/Abstract] 44

45 Querying PUBMED How many articles did Nunzio D Agostino publish? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] How manyof theseare reletedto EST? D'Agostino, Nunzio[Full Author Name] AND EST [Title/Abstract] How manyof theseare on the BMC GenomicsJournal? 45

46 Querying PUBMED How many articles did Nunzio D Agostino publish? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] How manyof theseare reletedto EST? D'Agostino, Nunzio[Full Author Name] AND EST [Title/Abstract] How manyof theseare on the BMC GenomicsJournal? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] AND BMC Genomics [journal] 46

47 Querying PUBMED How many articles did Nunzio D Agostino publish? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] How manyof theseare reletedto EST? D'Agostino, Nunzio[Full Author Name] AND EST [Title/Abstract] How manyof theseare on the BMC GenomicsJournal? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] AND BMC Genomics [journal] How many articles do include the word RNA-Seq in the title? 47

48 Querying PUBMED How many articles did Nunzio D Agostino publish? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] How manyof theseare reletedto EST? D'Agostino, Nunzio[Full Author Name] AND EST [Title/Abstract] How manyof theseare on the BMC GenomicsJournal? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] AND BMC Genomics [journal] How manyarticlesin PubMEDdo include the word RNA-Seq in the title? RNA-Seq[title] 48

49 Querying PUBMED How many articles did Nunzio D Agostino publish? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] How manyof theseare reletedto EST? D'Agostino, Nunzio[Full Author Name] AND EST [Title/Abstract] How manyof theseare on the BMC GenomicsJournal? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] AND BMC Genomics [journal] How manyarticlesin PubMEDdo include the word RNA-Seq in the title? RNA-Seq[title] How many reviews have been published in 2008 containing the word "transcriptome? 49

50 Querying PUBMED How many articles did Nunzio D Agostino publish? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] How manyof theseare reletedto EST? D'Agostino, Nunzio[Full Author Name] AND EST [Title/Abstract] How manyof theseare on the BMC GenomicsJournal? D'Agostino, Nunzio[Full Author Name] OR D Agostino, Nunzio[Full Author Name] AND BMC Genomics [journal] How manyarticlesin PubMEDdo include the word RNA-Seq in the title? RNA-Seq[title] How many reviews have been published in 2008 containing the word "transcriptome? transcriptome[title] AND review [Publication Type] AND 2008[publication date] 50

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