NCBI Molecular Biology Resources. NCBI Resources

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1 NBI Molecular Biology Resources A Field Guide NBI Resources The NBI Entrez System NBI Sequence Databases Primary data: GenBank Derivative data: RefSeq, Gene Protein Structure and Function Sequence polymorphisms and phenotypes NBI Genomic Resources BLAST 1

2 The National Institutes of Health Bethesda, MD WWW Access Entrez & BLAST 2

3 NBI Databases and Services GenBank largest sequence database Free public access to biomedical literature PubMed free Medline PubMed entral full text online access Entrez integrated molecular and literature databases BLAST highest volume sequence search service VAST structure similarity searches Software and Databases Sequencing enters ATT GA GA GA GA GA GTGA ATT ATT ATT ATT TTGAA GTGA ATT ATT GA GA GA GA AGTG AGTG Primary vs. Derivative Sequence Databases AGTG AGTG GTGA TTGAA GTGA TTGAA GenBank Updated ONLY by submitters Labs TTGAA AT ATT ATT GA GA GA GA urators Updated continually by NBI Algorithms RefSeq AGTGATA GATGAAA Genome Assembly UniGene 3

4 What is Entrez? A system of 31 linked databases A text search engine A tool for finding biologically linked data A retrieval engine A virtual workspace for manipulating large datasets Global Entrez Search Results 4

5 Entrez: Database Integration PubMed abstracts Word weight Homologene Gene 3-D Structure VAST Neighbors Related Structures BLAST Nucleotide sequences Neighbors Related Sequences Hard Link Protein sequences BLAST Neighbors Related Sequences BLink Domains Entrez Taxonomy The backbone of NBI [organism] 5

6 What is GenBank? NBI s Primary Sequence Database 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 NIH The International Sequence Database ollaboration Entrez Sequin BankIt ftp Submissions Updates NIG IB NBI getentry GenBank DDBJ Submissions Updates EMBL SRS EBI Submissions Updates EMBL 6

7 Organization of GenBank: Traditional Divisions Records are divided into 18 Divisions. 12 Traditional 6 Bulk Traditional Divisions: Direct Submissions (Sequin and BankIt) Accurate Well characterized PRI Primate PLN Plant and Fungal BT Bacterial and Archeal INV Invertebrate ROD Rodent VRL Viral VRT Other Vertebrate MAM Mammalian PHG Phage SYN Synthetic (cloning vectors) ENV Environmental Samples UNA Unannotated Entrez query: gbdiv_xxx[properties] Organization of GenBank: Bulk Divisions Records are divided into 18 Divisions. 12 Traditional 6 Bulk BULK Divisions: Batch Submission ( and FTP) Inaccurate Poorly characterized EST Expressed Sequence Tag GSS Genome Survey Sequence HTG High Throughput Genomic STS Sequence Tagged Site HT High Throughput cdna PAT Patent Entrez query: gbdiv_xxx[properties] 7

8 LOUS AF bp mrna linear PLN 29-JAN-2004 DEFINITION Prunus persica ethylene receptor (ETR1) mrna, complete cds. AESSION AF VERSION AF GI: KEYWORDS. SOURE Prunus persica (peach) ORGANISM Prunus persica Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; eurosids I; Rosales; Rosaceae; Amygdaloideae; Prunus. REFERENE 1 (bases 1 to 2540) AUTHORS Bassett,.L., Artlip,T.S. and allahan,a.m. TITLE haracterization of the peach homologue of the ethylene receptor, PpETR1, reveals some unusual features regarding transcript processing JOURNAL Planta 215 (4), (2002) PUBMED REFERENE 2 (bases 1 to 2540) AUTHORS Bassett,.B., Artlip,T.S. and Nickerson,M.L. TITLE Direct Submission JOURNAL Submitted (29-JAN-1999) Appalachian Fruit Research Station, USDA-ARS, 45 Wiltshire Road, Kearneysville, WV 25430, USA FEATURES Location/Qualifiers source /organism="prunus persica" /mol_type="mrna" /cultivar="loring" /db_xref="taxon:3760" /dev_stage="iii B/ fruit" gene /gene="etr1" DS /gene="etr1" /codon_start=1 /product="ethylene receptor" /protein_id="aaf " /db_xref="gi: " /translation="meaniepqwpadellmkyqyisdffialayfsipleliyfvk KSAVFPYRWVLVQFGAFIVLGATHLINLWTFSMHSRTVAIVMTTAKVLTAVVSATA LMLVHIIPDLLSVKTRELFLKNKAAELDREMGLIRTQEETGRHVRMLTHEIRSTLDRH TILKTTLVELGRTLALEEALWMPTRTGLELQLSYTLRQQNPVGYTVPIHLPVINQVF SSNRALKISPNSPVARMRPLAGKHMPGEVVAVRVPLLHLSNFQINDWPELSTKRYALM VLMLPSDSARQWHVHELELVEVVADQVAVALSHAAILEESMRARDLLMEQNIALDLAR REAETAIRARNDFLAVMNHEMRTPMHAIIALSSLLQETELTPEQRLMVETILKSSHLL ATLINDVLDLSRLEDGSLQLEIATFNLHSVFREVHNLIKPVASVKKLSVSLNLAADLP VQAVGDEKRLMQIVLNVVGNAVKFSKEGSISITAFVAKSESLRDFRAPEFFPAQSDNH FYLRVQVKDSGSGINPQDIPKLFTKFAQTQSLATRNSGGSGLGLAIKRFVNLMEGHI WIESEGPGKGTAIFIVKLGFAERSNESKLPFLTKVQANHVQTNFPGLKVLVMDDNGS VTKGLLVHLGDVTTVSSIDEFLHVISQEHKVVFMDVMPGIDGYELAVRIHEKFTKR HERPVLVALTGNIDKMTKENMRVGMDGVILKPVSVDKMRSVLSELLEHRVLFEAM" ORIGIN 1 gcacgagggc tcaccgagcg agctagctct tcaggagtca aggcttctgg gtgaggggaa 61 gaagaagaag cttctttgat gtgttggggt gccaatctaa agaggaagaa gaaggcctct 121 aatgtattga ggtcggctgt ctgggctgcc gatctgtgtt gaatggatag tttggtagag 181 atgcttcaac gacatagggt ggctgaaaag ggtttgaaga aagtgaagga ggaaaccaag tatactgaaa cctgtctcag ttgataaaat gaggagtgtt ttatcagaac tgttggagca 2461 tcgagtttta tttgaggcta tgtaagatat aggaaaattg ttctagtgaa ggaaagattt 2521 aaatggaaaa aaaaaaaaaa // A Traditional GenBank Record Header The Flatfile Format Feature Table Sequence Traditional GenBank Record AESSION U07418 VERSION U GI: Accession Stable Stable Reportable Universal Version Tracks Tracks changes in in sequence GI GI number NBI NBI internal internal use use well annotated well annotated the sequence is the data the sequence is the data 8

9 Bulk Divisions Batch Submission and htg ( and ftp) Inaccurate Poorly haracterized Expressed Sequence Tag 1 st pass single read cdna Genome Survey Sequence 1 st pass single read gdna High Throughput Genomic incomplete sequences of genomic clones Sequence Tagged Site PR-based mapping reagents GenBank File Formats ASN.1 The Raw Data flat file XML FASTA 9