1. Overview of Biological Databases (Lecture for CS498-CXZ Algorithms in Bioinformatics) Sept. 6, 2005 ChengXiang Zhai Department of Computer Science University of Illinois, Urbana-Champaign Most slides are taken from NCBI field guide at the web site http://www.ncbi.nlm.nih.gov/

2. The Central Dogma & Biological Data Protein structures -Experiments -Models (homologues) Literature information Original DNA Sequences (Genomes) Protein Sequences -Inferred -Direct sequencing Expressed DNA sequences ( = mRNA Sequences = cDNA sequences) Expressed Sequence Tags (ESTs)

3. Entrez Integrates Most of Them! Entrez Nucleotide PubMed Protein Taxonomy Structur e Domains3D Domains Journal s PMC OMIM Books PopSet SNP UniGene UniST S Genome Gene GEO GEO Datasets MeSH CancerChromosomes Homologen e

4. Outline NCBI & Entrez Major Biological Databases Using Entrez

5. Some background about Entrez…

6. The National Center for Biotechnology Information Created in 1988 as a part of the National Library of Medicine at NIH –Establish public databases –Research in computational biology –Develop software tools for sequence analysis –Disseminate biomedical information Bethesda,MD

7. Web Access: http://www.ncbi.nlm.nih.gov

9. Number of Users and Hits Per Day 1997 1998 1999 2000 2001 2002 2003 Christmas & New Year’s Days Currently averaging 10,000,000 to 50,000,000 hits per day!

10. Major Biological Databases

11. Entrez: Database Integration Hard Link Neighbors Related Structures 3 -D Structure VAST Neighbors Related Sequences NucleotideSequences BLAST Neighbors Related Sequences BLink Domains ProteinSequences BLAST Taxonomy Phylogeny PubMedAbstracts Word weight Related Articles Genome Gene OMIM Cancer Chromosome CDD 3D domain PubChem Books PMC OMIM SNP Genome Project HomoloGene UniGene GEO

12. Types of Databases Primary Databases –Original submissions by experimentalists –Content controlled by the submitter Examples: GenBank, SNP, GEO Derivative Databases –Built from primary data –Content controlled by third party (NCBI) Examples: Refseq, RefSNP, GEO Datasets, UniGene, TPA, NCBI Protein, Structure, Conserved Domain

13. Primary vs. Derivative Sequence DatabasesGenBank SequencingCenters GA ATT C C GA ATT C C AT GA ATT C C GA ATT C C TTGACA ATTGACTA ACGTGC TTGACA CGTGA ATTGACTA TATAGCCG ACGTGC TTGACA CGTGA ATTGACTA TATAGCCG C ATT GA ATT C C GA ATT C C Labs Algorithms UniGene Curators RefSeq Genome Assembly TATAGCCG AGCTCCGATA CCGATGACAA Updated continually by NCBI Updated ONLY by submitters

14. Entrez Nucleotides Primary GenBank / EMBL / DDBJ 57,172,944 Derivative RefSeq 1,278,742 Third Party Annotation 4,653 PDB 5,973 Total 58,462,312

15. Entrez Protein: Derivative Databases GenPept 3,515,141 RefSeq 1,802,523 Third Party Annotation 4,217 Swiss Prot 189,324 PIR 222,232 PRF 12,079 PDB 68,621 Total 5,814,137 BLAST nr total 2,726,372

16. Database 1: GenBank NCBI’s Primary Sequence Database

17. What is GenBank? Nucleotide only sequence database Archival in nature –Historical –Reflective of submitter point of view (subjective) –Redundant GenBank Data –Direct submissions (traditional records) –Batch submissions (EST, GSS, STS) –ftp accounts (genome data) Three collaborating databases –GenBank –DNA Database of Japan (DDBJ) –European Molecular Biology Laboratory (EMBL) Database

18. EBI GenBank DDBJ EMBL EMBL Entrez SRS getentry NIG CIB NCBI NIH Submissions Updates Submissions Updates Submissions Updates International Sequence Database Collaboration

19. GenBank Divisions “Organismal” PRI (28) Primate ROD (15) Rodent PLN (13) Plant and Fungal BCT (11) Bacterial/Archeal INV (7) Invertebrate VRT (7) Other Vertebrate VRL (4) Viral MAM (2) Mammalian PHG (1) Phage SYN (1) Synthetic UNA (1) Unannotated “Functional” EST (377) Expressed Sequence Tag GSS (138) Genome Survey Sequence HTG (63) High Throughput Genomic PAT (17) Patent STS (9) Sequence Tagged Site CON (1) Contigs, virtual Organized by taxonomy (sort of) Direct submissions (Sequin/Bankit) Accurate (~1 error per 10,000 bp) Well characterized Organized by sequence type Batch submissions (ftp/email) Inaccurate Poorly characterized

20. GenBank Functional (Bulk) Divisions GenBank EST STS GSS HTG Expressed Sequence Tag –1st pass single read cDNA Genome Survey Sequence –1st pass single read gDNA High Throughput Genomic –incomplete sequences of genomic clones Sequence Tagged Site –PCR-based mapping reagents Whole Genome Shotgun

21. EST Division: Expressed Sequence Tags RNA gene products nucleus 30,000 genes 80-100,000 unique cDNA clones in library - isolate unique clones - sequence once from each end make cDNA library 5’ 3’ >IMAGE:275615 3', mRNA sequence NNTCAAGTTTTATGATTTATTTAACTTGTGGAACAAAAATAAACCAGATTAACCACAACCATGCCTTA TTATCAAATGTATAAGANGTAAATATGAATCTTATATGACAAAATGTTTCATTCATTATAACAAATTT AATAATCCTGTCAATNATATTTCTAAATTTTCCCCCAAATTCTAAGCAGAGTATGTAAATTGGAAGTT CTTATGCACGCTTAACTATCTTAACAAGCTTTGAGTGCAAGAGATTGANGAGTTCAAATCTGACCAAG GTTGATGTTGGATAAGAGAATTCTCTGCTCCCCACCTCTANGTTGCCAGCCCTC >IMAGE:275615 5' mRNA sequence GACAGCATTCGGGCCGAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCTACTCTCTCTTTCTGG TGGAGGTATCCAGCGTACTCCAAAGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAA TTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGA GAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTAC TGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTTGAACCATGTNGACTTTGTCACAGNC AAGTTNAGTTTAAGTGGGNATCGAGACATGTAAGGCAGGCATCATGGGAGGTTTTGAAGNATGCCGCN TTGGATTGGGATGAATTCCAAATTTCTGGTTTGCTTGNTTTTTTAATATTGGATATGCTTTTG

22. ESTs in Entrez Total 28 million records Human 6.0 million Mouse 4.3 million Rat 0.7 million Zebrafish 0.6 million Wheat0.6 million Barley0.3 million Maize0.4 million Total 28 million records Human 6.0 million Mouse 4.3 million Rat 0.7 million Zebrafish 0.6 million Wheat0.6 million Barley0.3 million Maize0.4 million

23. GSS, WGS, HTG shred Whole BAC insert (or genome) isolate clonessequence GSS division or trace archive Draft sequence ( HTG division ) assembly whole genome shotgun assemblies (traditional division)

24. HTG Example: Honeybee Draft Sequences Unfinished sequences of BACs Gaps and unordered pieces Finished sequences (Phase 3) move to traditional GenBank division Unfinished sequences of BACs Gaps and unordered pieces Finished sequences (Phase 3) move to traditional GenBank division LOCUS AC141845 147720 bp DNA linear HTG 19-MAR-2004 DEFINITION Apis mellifera clone CH224-4A2, WORKING DRAFT SEQUENCE, 14 unordered pieces. ACCESSION AC141845 VERSION AC141845.1 GI:29124029 KEYWORDS HTG; HTGS_PHASE1; HTGS_DRAFT. LOCUS AC141845 147720 bp DNA linear HTG 19-MAR-2004 DEFINITION Apis mellifera clone CH224-4A2, WORKING DRAFT SEQUENCE, 14 unordered pieces. ACCESSION AC141845 VERSION AC141845.1 GI:29124029 KEYWORDS HTG; HTGS_PHASE1; HTGS_DRAFT.

25. Sequence Records (millions) Total Base Pairs (billions) 0 5 10 15 20 25 30 35 0 5 10 15 20 25 30 35 40 Sequence records Total base pairs Release 148: 45.2 million records 49.4 billion nucleotides Average doubling time ≈ 14 months ’83 ’84 ’85 ’86 ’87 ’88 ’89 ’90 ’91 ’92 ’93 ’94 ’95 ’96 ’97 ’98 ’99 ’00 ’01 ’02 ’03 ’04 ’05 ’06 40 45 50 55 50

26. File Formats of the Sequence Databases Each sequence is represented by a text record called a flat file. GenBank/GenPept (useful for scientists) FASTA (the simplest format) ASN.1 & XML (useful for programmers)

27. A Traditional GenBank Record LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004 DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds. ACCESSION AY182241 VERSION AY182241.2 GI:32265057 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, 84-94 (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, 10300 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, 10300 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:27804758. FEATURES Location/Qualifiers source 1..1931 /organism="Malus x domestica" /mol_type="mRNA" /cultivar="'Law Rome'" /db_xref="taxon:3750" /tissue_type="peel" gene 1..1931 /gene="AFS1" CDS 54..1784 /gene="AFS1" /note="terpene synthase" /codon_start=1 /product="(E,E)-alpha-farnesene synthase" /protein_id="AAO22848.2" /db_xref="GI:32265058" /translation="MEFRVHLQADNEQKIFQNQMKPEPEASYLINQRRSANYKPNIWK NDFLDQSLISKYDGDEYRKLSEKLIEEVKIYISAETMDLVAKLELIDSVRKLGLANLF EKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQHGYKVSQDIFGRFMDEKGTLE 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 // Header Feature Table Sequence The Flatfile Format

28. LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004 DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds. ACCESSION AY182241 VERSION AY182241.2 GI:32265057 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, 84-94 (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, 10300 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, 10300 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:27804758. The Header

29. LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004 DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds. ACCESSION AY182241 VERSION AY182241.2 GI:32265057 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, 84-94 (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, 10300 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, 10300 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:27804758. Header: Locus Line LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004 Molecule type Division Modification Date Locus name Length

30. LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004 DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds. ACCESSION AY182241 VERSION AY182241.2 GI:32265057 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, 84-94 (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, 10300 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, 10300 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:27804758. Header: Database Identifiers ACCESSION AY182241 VERSION AY182241.2 GI:32265057 ACCESSION AY182241 VERSION AY182241.2 GI:32265057 Accession Stable Reportable Universal Accession Stable Reportable Universal Version Tracks changes in sequence Version Tracks changes in sequence GI number NCBI internal use GI number NCBI internal use

31. LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004 DEFINITION Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds. ACCESSION AY182241 VERSION AY182241.2 GI:32265057 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, 84-94 (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, 10300 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, 10300 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:27804758. Header: Organism 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. 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. NCBI-controlled taxonomy

32. FEATURES Location/Qualifiers source 1..1931 /organism="Malus x domestica" /mol_type="mRNA" /cultivar="'Law Rome'" /db_xref="taxon:3750" /tissue_type="peel" gene 1..1931 /gene="AFS1" CDS 54..1784 /gene="AFS1" /note="terpene synthase" /codon_start=1 /product="(E,E)-alpha-farnesene synthase" /protein_id="AAO22848.2" /db_xref="GI:32265058" /translation="MEFRVHLQADNEQKIFQNQMKPEPEASYLINQRRSANYKPNIWK NDFLDQSLISKYDGDEYRKLSEKLIEEVKIYISAETMDLVAKLELIDSVRKLGLANLF EKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQHGYKVSQDIFGRFMDEKGTLE NHHFAHLKGMLELFEASNLGFEGEDILDEAKASLTLALRDSGHICYPDSNLSRDVVHS LELPSHRRVQWFDVKWQINAYEKDICRVNATLLELAKLNFNVVQAQLQKNLREASRWW ANLGIADNLKFARDRLVECFACAVGVAFEPEHSSFRICLTKVINLVLIIDDVYDIYGS EEELKHFTNAVDRWDSRETEQLPECMKMCFQVLYNTTCEIAREIEEENGWNQVLPQLT KVWADFCKALLVEAEWYNKSHIPTLEEYLRNGCISSSVSVLLVHSFFSITHEGTKEMA DFLHKNEDLLYNISLIVRLNNDLGTSAAEQERGDSPSSIVCYMREVNASEETARKNIK GMIDNAWKKVNGKCFTTNQVPFLSSFMNNATNMARVAHSLYKDGDGFGDQEKGPRTHI LSLLFQPLVN" The Feature Table Coding sequence start (atg) stop (tag) Implied protein Implied protein GenPept Identifiers

33. The Sequence: 99.99% Accurate 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 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 1741 ggacccacat cctgtcttta ctattccaac ctcttgtaaa ctagtactca tatagtttga 1801 aataaatagc agcaaaagtt tgcggttcag ttcgtcatgg ataaattaat ctttacagtt 1861 tgtaacgttg ttgccaaaga ttatgaataa aaagttgtag tttgtcgttt aaaaaaaaaa 1921 aaaaaaaaaa a // 1741 ggacccacat cctgtcttta ctattccaac ctcttgtaaa ctagtactca tatagtttga 1801 aataaatagc agcaaaagtt tgcggttcag ttcgtcatgg ataaattaat ctttacagtt 1861 tgtaacgttg ttgccaaaga ttatgaataa aaagttgtag tttgtcgttt aaaaaaaaaa 1921 aaaaaaaaaa a //

34. GenPept: FASTA format >gi|32265058|gb|AAO22848.2| (E,E)-alpha-farnesene synthase [Malus x domestica] MEFRVHLQADNEQKIFQNQMKPEPEASYLINQRRSANYKPNIWKNDFLDQSLISKYDGDEYRKLSEKLIE EVKIYISAETMDLVAKLELIDSVRKLGLANLFEKEIKEALDSIAAIESDNLGTRDDLYGTALHFKILRQH GYKVSQDIFGRFMDEKGTLENHHFAHLKGMLELFEASNLGFEGEDILDEAKASLTLALRDSGHICYPDSN LSRDVVHSLELPSHRRVQWFDVKWQINAYEKDICRVNATLLELAKLNFNVVQAQLQKNLREASRWWANLG IADNLKFARDRLVECFACAVGVAFEPEHSSFRICLTKVINLVLIIDDVYDIYGSEEELKHFTNAVDRWDS RETEQLPECMKMCFQVLYNTTCEIAREIEEENGWNQVLPQLTKVWADFCKALLVEAEWYNKSHIPTLEEY LRNGCISSSVSVLLVHSFFSITHEGTKEMADFLHKNEDLLYNISLIVRLNNDLGTSAAEQERGDSPSSIV CYMREVNASEETARKNIKGMIDNAWKKVNGKCFTTNQVPFLSSFMNNATNMARVAHSLYKDGDGFGDQEK GPRTHILSLLFQPLVN >gi|32265070|gb|AAP75563.1| putative doublecortin domain-containing protein MAKTGAEDHREALSQSSLSLLTEAMEVLQQSSPEGTLDGNTVNPIYKYILNDLPREFMSSQAKAVIKTTD DYLQSQFGPNRLVHSAAVSEGSGLQDCSTHQTASDHSHDEISDLDSYKSNSKNNSCSISASKRNRPVSAP VGQLRVAEFSSLKFQSARNWQKLSQRHKLQPRVIKVTAYKNGSRTVFARVTAPTITLLLEECTEKLNLNM AARRVFLADGKEALEPEDIPHEADVYVSTGEPFLNPFKKIKDHLLLIKKVTWTMNGLMLPTDIKRRKTKP VLSIRMKKLTERTSVRILFFKNGMGQDGHEITVGKETMKKVLDTCTIRMNLNLPARYFYDLYGRKIEDIS KGKH

35. Seq-entry ::= set { class nuc-prot, descr { title "Malus x domestica (E,E)-alpha-farnesene synthase (AFS1) mRNA, complete cds.", source { org { taxname "Malus x domestica", common "cultivated apple", db { { db "taxon", tag id 3750 } }, orgname { name binomial { genus "Malus", species "x domestica" }, mod { { subtype cultivar, subname "'Law Rome'" }, { subtype old-name, subname "Malus domestica", attrib "(10)cultivar='Law Rome'" } }, lineage "Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; rosids; eurosids I; Rosales; Rosaceae; Maloideae; Malus", gcode 1,, Abstract Syntax Notation: ASN.1 FASTA Nucleotide FASTA Nucleotide FASTA Protein FASTA Protein GenPept GenBank ASN.1

36. Database 2: RefSeq NCBI’s Derivative Sequence Database

37. What is RefSeq? Curated transcripts and proteins (NM_, NP_) –reviewed –human, mouse, rat, fruit fly, zebrafish, arabidopsis microbial genomes (proteins), and more Model transcripts and proteins (XM_, XP_) Assembled Genomic Regions (contigs) (NT_, NW_) –human genome –mouse genome –rat genome Chromosome records (NC_) –Human genome –microbial –organelle ftp://ftp.ncbi.nih.gov/refseq/release / srcdb_refseq[Properties]

38. RefSeq Benefits non-redundancy explicitly linked nucleotide and protein sequences updates to reflect current sequence data and biology data validation format consistency distinct accession series stewardship by NCBI staff and collaborators

39. Curated genomic DNA (NC, NT, NW) Curated Model mRNA (XM) (XR) Curated mRNA (NM) (NR) Model protein (XP) RefSeq Curation Processes Protein (NP) Scanning....

40. RefSeq Accession Numbers mRNAs and Proteins NM_123456 Curated mRNA NP_123456 Curated Protein NR_123456 Curated non-coding RNA XM_123456 Predicted mRNA XP_123456 Predicted Protein XR_123456 Predicted non-coding RNA Gene Records NG_123456 Reference Genomic Sequence Chromosome NC_123455 Microbial replicons, organelle, viral genomes, human chromosomes Assemblies NT_123456 Contig NW_123456 WGS Supercontig

41. From GenBank to RefSeq

42. NM_000121: Sequence Revision History

44. Database 3: UniGene NCBI’s Derivative EST Database

45. UniGene Records are clusters of mRNAs and ESTs that ideally represent single genes Records are created automatically by a modified BLAST algorithm UniGene provides a means to identify an EST or unannotated mRNA Clustering Expressed Sequences

46. Gene-oriented clusters of expressed sequences Automatic clustering using MegaBlast Each cluster represents a unique gene Informed by genome hits Information on tissue types and map locations Useful for gene discovery and selection of mapping reagents UniGene unique gene

47. A Cluster of ESTs query 5’ EST hits 3’ EST hits

48. UniGene Collections

49. Example UniGene Cluster

50. Histogram of cluster sizes for UniGene Hs Build 177 (Now at Build #186)

51. UniGene Cluster Hs.95351 SELECTED PROTEIN SIMILARITES

52. UniGene Cluster Hs.95351 GENE EXPRESSION

53. UniGene Cluster Hs.95351: expression

54. UniGene Cluster Hs.95351: seqs

55. Download sequences web page ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/

56. Database 4: MMDB NCBI’s derivative protein structure database

57. Indexing into MMDB Structure id 1, name "helix 1", type helix, location subgraph residues interval { { molecule-id 1, from 49, to 61 } } }, Add secondary structure inter-residue-bonds { { atom-id-1 { molecule-id 1, residue-id 1, atom-id 1 }, atom-id-2 { molecule-id 1, residue-id 2, atom-id 9 } }, Add chemical bonds Import only experimentally determined structures Convert to ASN.1 Verify sequences Create “backbone” model (Cα, P only) Create single-conformer model MMDB Molecular Modeling Data Base

58. Structure Summary Cn3D viewer Conserved Domains 3D Domain Neighbors Structure Neighbors

59. Cn3D 4.1: C-Src

60. Cn3D 4.1: Structural Alignment Casein kinase S. pombe Src Kinase H. sapiens Conserved ATP binding site

61. Cn3D: Simple Homology Modeling human swordtail

62. NCBI CD: Tyrosine Kinase

63. Using Cn3D to model domains

64. Submitting a PDB File to VAST Choose the file format Remove all lines except ATOM This is the best way to convert PDB files to MMDB format for viewing with Cn3D!

65. Database 5: GEO NCBI’s Gene Expression Omnibus

66. GPL Platform descriptions GSM Raw/processed spot intensities from a single slide/chip GSE Grouping of slide/chip data “a single experiment” GDS Grouping of experiments Curated by NCBI Submitted by Experimentalists Submitted by Manufacturer* Entrez GEO Entrez GEO Datasets G EO S a M ple : experimental conditions G EO SE ries : set of related samples

67. What’s a DataSet? Platform (GPL) array definition Sample (GSM) hyb. measurements Series (GSE) related Samples Supplied by submitter DataSet (GDS) A collection of experimentally-related samples processed using the same platform. Samples within DataSets are organized into subgroups based on experimental variables. Form the basis of GEO’s query, analysis and data display tools. Assembled by GEO staff

68. Gene Expression Omnibus Dataset browser

69. GEO Dataset Browser

70. GEO Dataset Report

71. GEO Profiles … of 12625

72. Database 6: CDD NCBI’s Derivative Conserved Domain Database

73. Entrez CDD

74. Conserved Domain Database Multiple sequence alignments Position-specific scoring matrices (PSSM) Sources SMART, PFAM, COGs, KOGs, and NCBI curated domains (structure-informed alignments) Multiple sequence alignments Position-specific scoring matrices (PSSM) Sources SMART, PFAM, COGs, KOGs, and NCBI curated domains (structure-informed alignments)

75. CDD >gi|45549418|gb|AAS67634.1| ATP7A [Solenodon paradoxus] IVYQPHLITVEEIKKQIKAVGFPAFIKKQPKYLKLGAIDIERLKNIPVKSSEGSQQMSPS STNDSKVTLTIDGMHCNSCVSNIESALSTLHYVSSIVVSLQNKSAIIKYNANSVTPEIL KKAIEAISPGQYRVSITSEVESTSNSPSSSSQKAPLNVVSQPLTQVTVININGMTCNS CVQSIEGVMSKKAGVKSIQVSLANRNGTVEYDP LLTSPEILRE

76. CDD CD Pfam COG Click on a colored bar to align your sequence to the CD

77. Conserved Domain Database: cd00371.1, HMA

78. CDD

79. CDART: Conserved Domain Architecture Retrieval Tool

80. Database 7: NCBI Genome Map

81. Viewing Complex Genomes Map Viewer Home Page Shows all supported organisms Provides links to genomic BLAST –Genome Overview Page Provides links to individual chromosomes Shows hits on a genome graphically –Chromosome Viewing Page Allows interactive views of annotation details Provides numerous maps unique to each genome NCBI Map Viewer

82. The Map Viewer Genome BLAST

83. Map Viewer: Human MLH1 Customizable NCBI Assembly EST Hits Gene Annotations Models Transcripts

84. Maps and Options

85. Mapped Variations

86. MLH1 Synteny: Mammalian Genomes

87. Many Other NCBI Databases…

88. Other Specialized Databases Gene Symbol Database ( HUGO Gene Nomenclature )HUGO Gene Nomenclature KEGG (Kyoto Encyclopedia of Genes and Genomes) Pathway KEGG EPD (Eukaryote Promoter Database) EPD Transcription Factor Database ( TRANSFAC )TRANSFAC Many organism-specific databases (e.g., Flybase, Beebase)Flybase Beebase …

89. Access Databases through Entrez

90. Accessing the Data in Entrez Web Tools –Batch Entrez Upload a file of GI or accession numbers to retrieve sequences –Batch Citation Matcher Send citation information to Entrez and retrieve PubMed IDs for linking, citation display or other applications –Advanced Entrez Searching Advanced searching techniques for Web Entrez –My NCBI Includes automatic e-mailing of search updates and filters for search results Requires a username and password to access stored searches Programming Tools –E-Utilities Run Entrez queries and download data from your own scripts over the Web –Linking to Entrez Link to specific Entrez pages from your own web pages or applications –Entrez Client/Server C language library for embedding Entrez calls into your programs

91. Entrez: Web Access Default search: Against all databases in Entrez Interface: Global Entrez Target database: Adjustable using the pull-down menu Default search: Against all databases in Entrez Interface: Global Entrez Target database: Adjustable using the pull-down menu

92. /************************************************************************ * * asn2ff.c * convert an ASN.1 entry to flat file format, using the FFPrintArray. * **************************************************************************/ #include #include "asn2ff.h" #include "asn2ffp.h" #include "ffprint.h" #include #ifdef ENABLE_ID1 #include #endif FILE *fpl; Args myargs[] = { {"Filename for asn.1 input","stdin",NULL,NULL,TRUE,'a',ARG_FILE_IN,0.0,0,NULL}, {"Input is a Seq-entry","F", NULL,NULL,TRUE,'e',ARG_BOOLEAN,0.0,0,NULL}, {"Input asnfile in binary mode","F",NULL,NULL,TRUE,'b',ARG_BOOLEAN,0.0,0,NULL}, {"Output Filename","stdout", NULL,NULL,TRUE,'o',ARG_FILE_OUT,0.0,0,NULL}, {"Show Sequence?","T", NULL,NULL,TRUE,'h',ARG_BOOLEAN,0.0,0,NULL}, Toolbox Sources ftp> open ftp.ncbi.nih.gov. ftp> cd toolbox ftp> cd ncbi_tools ftp://ftp.ncbi.nlm.gov/toolbox/ncbi_tools NCBI Toolbox

94. Challenges in Bioinformatics Hard Link Neighbors Related Structures 3 -D Structure VAST Neighbors Related Sequences NucleotideSequences BLAST Neighbors Related Sequences BLink Domains ProteinSequences BLAST Taxonomy Phylogeny PubMedAbstracts Word weight Related Articles Genome Gene OMIM Cancer Chromosome CDD 3D domain PubChem Books PMC OMIM SNP Genome Project HomoloGene UniGene GEO How can we help biologists manage and exploit all such rapid growing, heterogeneous, and inaccurate information both efficiently and effectively?