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Overview of Biological Databases

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/.

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Overview of Biological Databases

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  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 Original DNA Sequences (Genomes) Expressed DNA sequences ( = mRNA Sequences = cDNA sequences) Expressed Sequence Tags (ESTs) • Protein Sequences • Inferred • Direct sequencing • Protein structures • Experiments • Models (homologues) Literature information

  3. Entrez Integrates Most of Them! Gene UniGene CancerChromosomes UniSTS Homologene SNP PopSet Genome Nucleotide GEO Books Entrez Taxonomy PubMed GEO Datasets MeSH OMIM Protein PMC Journals Domains 3D Domains Structure

  4. Outline • NCBI & Entrez • Major Biological Databases • Using Entrez

  5. Some background about Entrez…

  6. The National Center for Biotechnology Information Bethesda,MD 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

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

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

  9. Major Biological Databases

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

  11. 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

  12. ACGTGC C C GA GA ATT GA GA C ATT TATAGCCG AGCTCCGATA CCGATGACAA RefSeq C TATAGCCG ACGTGC Curators CGTGA ATTGACTA TTGACA Genome Assembly TTGACA TTGACA ACGTGC ACGTGC TATAGCCG CGTGA CGTGA TATAGCCG ATTGACTA TATAGCCG ATTGACTA ATTGACTA CGTGA ATTGACTA ATTGACTA ATT TATAGCCG TATAGCCG TATAGCCG TATAGCCG TATAGCCG TTGACA C GenBank UniGene GA AT C C C C ATT GA GA GA GA ATT ATT ATT Algorithms GA GA GA GA C C ATT ATT C C Primary vs. DerivativeSequence Databases Labs Sequencing Centers Updated continually by NCBI Updated ONLY by submitters

  13. 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

  14. Entrez Protein: Derivative Databases

  15. Database 1: GenBankNCBI’s Primary Sequence Database

  16. 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

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

  18. 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 • Organized by taxonomy (sort of) • Direct submissions (Sequin/Bankit) • Accurate (~1 error per 10,000 bp) • Well characterized “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 sequence type • Batch submissions (ftp/email) • Inaccurate • Poorly characterized

  19. EST GenBank GSS HTG STS GenBank Functional (Bulk) Divisions • 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

  20. 5’ 3’ make cDNA library 80-100,000 unique cDNA clones in library EST Division: Expressed Sequence Tags >IMAGE:275615 5' mRNA sequence GACAGCATTCGGGCCGAGATGTCTCGCTCCGTGGCCTTAGCTGTGCTCGCGCTACTCTCTCTTTCTGG TGGAGGTATCCAGCGTACTCCAAAGATTCAGGTTTACTCACGTCATCCAGCAGAGAATGGAAAGTCAA TTCCTGAATTGCTATGTGTCTGGGTTTCATCCATCCGACATTGAAGTTGACTTACTGAAGAATGGAGA GAATTGAAAAAGTGGAGCATTCAGACTTGTCTTTCAGCAAGGACTGGTCTTTCTATCTCTTGTACTAC TGAATTCACCCCCACTGAAAAAGATGAGTATGCCTGCCGTGTTGAACCATGTNGACTTTGTCACAGNC AAGTTNAGTTTAAGTGGGNATCGAGACATGTAAGGCAGGCATCATGGGAGGTTTTGAAGNATGCCGCN TTGGATTGGGATGAATTCCAAATTTCTGGTTTGCTTGNTTTTTTAATATTGGATATGCTTTTG nucleus 30,000 genes gatccantgccatacg ctcgccaattcnntcg • - isolate unique clones • sequence once from each end >IMAGE:275615 3', mRNA sequence NNTCAAGTTTTATGATTTATTTAACTTGTGGAACAAAAATAAACCAGATTAACCACAACCATGCCTTA TTATCAAATGTATAAGANGTAAATATGAATCTTATATGACAAAATGTTTCATTCATTATAACAAATTT AATAATCCTGTCAATNATATTTCTAAATTTTCCCCCAAATTCTAAGCAGAGTATGTAAATTGGAAGTT CTTATGCACGCTTAACTATCTTAACAAGCTTTGAGTGCAAGAGATTGANGAGTTCAAATCTGACCAAG GTTGATGTTGGATAAGAGAATTCTCTGCTCCCCACCTCTANGTTGCCAGCCCTC RNA gene products

  21. ESTs in Entrez Total 28 million records Human 6.0 million Mouse 4.3 million Rat 0.7 million Zebrafish 0.6 million Wheat 0.6 million Barley 0.3 million Maize 0.4 million

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

  23. 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. HTG Example: Honeybee Draft Sequences • Unfinished sequences of BACs • Gaps and unordered pieces • Finished sequences (Phase 3) move to traditional GenBank division

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

  25. File Formats of theSequence 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)

  26. Header Feature Table Sequence A TraditionalGenBank 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 // The Flatfile Format

  27. The Header 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.

  28. Length Division Molecule type Locus name Modification Date Header: Locus Line 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. LOCUS AY182241 1931 bp mRNA linear PLN 04-MAY-2004

  29. Header: Database Identifiers 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. • Accession • Stable • Reportable • Universal ACCESSION AY182241 VERSION AY182241.2 GI:32265057 Version Tracks changes in sequence GI number NCBI internal use

  30. Header: Organism 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. 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

  31. GenPept Identifiers Implied protein The Feature Table 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" start (atg) stop (tag) Coding sequence

  32. 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 1741 ggacccacat cctgtcttta ctattccaac ctcttgtaaa ctagtactca tatagtttga 1801 aataaatagc agcaaaagtt tgcggttcag ttcgtcatgg ataaattaat ctttacagtt 1861 tgtaacgttg ttgccaaaga ttatgaataa aaagttgtag tttgtcgttt aaaaaaaaaa 1921 aaaaaaaaaa a //

  33. 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

  34. GenPept GenBank ASN.1 FASTA Protein FASTA Nucleotide Abstract Syntax Notation: ASN.1 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 ,,

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

  36. 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 srcdb_refseq[Properties] ftp://ftp.ncbi.nih.gov/refseq/release/

  37. 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

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

  39. RefSeq Accession Numbers mRNAs and Proteins NM_123456Curated mRNA NP_123456Curated Protein NR_123456Curated non-coding RNA XM_123456Predicted mRNA XP_123456Predicted Protein XR_123456Predicted non-coding RNA Gene Records NG_123456Reference Genomic Sequence Chromosome NC_123455Microbial replicons, organelle , viral genomes, human chromosomes Assemblies NT_123456Contig NW_123456WGSSupercontig

  40. From GenBank to RefSeq

  41. NM_000121: Sequence Revision History

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

  43. UniGene Clustering Expressed Sequences • 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

  44. UniGene 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 unique gene

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

  46. UniGene Collections

  47. Example UniGene Cluster

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

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