1. Databases

2. Where to get data? GenBank –http://www.ncbi.nlm.nih.govhttp://www.ncbi.nlm.nih.gov Protein Databases –SWISS-PROT: http://www.expasy.ch/sprothttp://www.expasy.ch/sprot –PDB: http://www.pdb.gov/http://www.pdb.gov/ And many others

3. Bibliograph y

4. Growth in genome sequencing

5. Working Draft Sequence gaps

6. The reagent: databases Organized array of information Place where you put things in, and (if all is well) you should be able to get them out again. Resource for other databases and tools. Simplify the information space by specialization. Bonus: Allows you to make discoveries.

7. Contains files or tables, each containing numerous records and fields Simplest form, either a large single text file or collection of text files Commonest type, stores the data within a number of tables (with records and fields). Each table will link each other by a shared file called a key

8. Flat file Relational database model The operators are written in query-specific languages based on relational algebra Structured Query Language (SQL) is commonly used

9. XML (eXtensible Markup Language) is now a general tool for storage of data and information. HTML and XHTML are subsets of XML. The key feature is to use identifiers called tabs Understanding Bioinformatics tag can be defined and used to identify book publishers Extraction from XML file is similar to database querying.

10. Databases Information system Query system Storage System Data GenBank flat file PDB file Interaction Record Title of a book Book

11. Databases Information system Query system Storage System Data Boxes Oracle MySQL PC binary files Unix text files Bookshelves

12. Databases Information system Query system Storage System Data A List you look at A catalogue indexed files SQL grep

13. The UBC library Google Entrez SRS Databases Information system Query system Storage System Data

14. Bioinformatics Information Space July 17, 1999 Nucleotide sequences:4,456,822 Protein sequences: 706,862 3D structures: 9,780 Human Unigene Clusters: 75,832 Maps and Complete Genomes: 10,870 Different species node: 52,889 dbSNP 6,377 RefGenes 515 human contigs > 250 kb 341 (4.9MB) PubMed records: 10,372,886 OMIM records: 10,695

15. The challenge of the information space: Nucleotide records 36,653,899 Protein sequences 4,436,362 3D structures 19,640 Interactions & complexes 52,385 Human Unigene Cluster 118,517 Maps and Complete Genomes 6,948 Different taxonomy Nodes 283,121 Human dbSNP 13,179,601 Human RefSeq records 22,079 bp in Human Contigs > 5,000 kb (116) 2,487,920,000 PubMed records 12,570,540 OMIM records 15,138 Feb 10 2004

16. From a CBW student course evaluation: “I could probably live the rest of my life happily without ever seeing the ‘growth of GenBank’ curve … again.”

17. Databases Primary (archival) –GenBank/EMBL/DDBJ –UniProt –PDB –Medline (PubMed) –BIND Secondary (curated) –RefSeq –Taxon –UniProt –OMIM –SGD

18. http://nar.oupjournals.org/content/vol31/issue1/

19. Databases –PubMed and other NCBI databases –Biochemical databases –Protein domain databases –Structural databases –Genome comparison databases Tools –CDD / COGs –VAST / FSSP Tools of trade for the “armchair scientist”

20. Distribution of the type of databases as classified at the NAR database web site

22. Archival or Primary Data –Text: PubMed –DNA Sequence: GenBank –Protein Sequence: Entrez Proteins, TREMBL –Protein Structures: PDB Curated or Processed Data –DNA sequences : RefSeq, LocusLink, OMIM –Protein Sequences: SWISS-PROT, PIR –Protein Structures : SCOP, CATH, MMDB –Genomes: Entrez Genomes, COGs Types of databases Nucleic Acids Research: Database Issue each January 1 Articles on ~100 different databases

23. 4 ways to access protein and DNA sequences [1] LocusLink with RefSeq [2] Entrez [3] UniGene UniGene collects expressed sequence tags (ESTs) into clusters, in an attempt to form one gene per cluster. Use UniGene to study where your gene is expressed in the body, when it is expressed, and see its abundance. [4] ExPASy SRS

24. 4 ways to access protein and DNA sequences [1] LocusLink with RefSeq [2] Entrez [3] UniGene [4] ExPASy SRS There are many bioinformatics servers outside NCBI. Try ExPASy’s sequence retrieval system at http://www.expasy.ch/ (ExPASy = Expert Protein Analysis System) Or try ENSEMBL at www.ensembl.org for a premier human genome web browser.

25. National Center for Biotechnology Information (NCBI) www.ncbi.nlm.nih.gov Page 24

26. The National Center for Biotechnology Information (NCBI) Created as a part of the National Library of Medicine, National Institutes of Health in 1988 –Establish public databases –Research in computational biology –Develop software tools for sequence analysis –Disseminate biomedical information Tools: BLAST(1990), Entrez (1992) GenBank (1992) Free MEDLINE (PubMed, 1997) Other databases: dbEST, dbGSS, dbSTS, MMDB, OMIM, UniGene, Taxonomy, GeneMap, SAGE, LocusLink, RefSeq

27. What is GenBank? Archival nucleotide sequence database Sample slogans: “Easy deposits, unlimited withdrawals, high interest”, “All bases covered”, “Billions and billions served” Data are shared nightly among three collaborating databases: GenBank at NCBI - Bethesda, Maryland, USA DNA Database of Japan (DDBJ) at NIG - Mishima, Japan European Molecular Biology Laboratory Database European Molecular Biology Laboratory Database (EMBL) at EBI - Hinxton, UK

28. Some guiding principles of working with GenBank GenBank is a nucleotide-centric view of the information space GenBank is a repository of all publically available sequences In GenBank, records are grouped for various reasons Data in GenBank is only as good as what you put in

29. NCBI databases and their links Word Weight VAST BLASTBLAST Phylogeny Genomes Taxonomy Nucleotide Sequences Protein Sequences Article Abstracts Medline 3-D Structure 3 D Structure MMDB

30. www.ncbi.nlm.nih.gov Fig. 2.5 Page 25

31. Fig. 2.5 Page 25

32. PubMed is… National Library of Medicine's search service 16 million citations in MEDLINE links to participating online journals PubMed tutorial (via “Education” on side bar) Page 24

33. Entrez integrates… the scientific literature; DNA and protein sequence databases; 3D protein structure data; population study data sets; assemblies of complete genomes Page 24

34. Entrez is a search and retrieval system that integrates NCBI databases Page 24

35. Entrez: An integrated search and retrieval system

36. BLAST is… Basic Local Alignment Search Tool NCBI's sequence similarity search tool supports analysis of DNA and protein databases 100,000 searches per day Page 25

37. OMIM is… Online Mendelian Inheritance in Man catalog of human genes and genetic disorders edited by Dr. Victor McKusick, others at JHU Page 25

38. OMIM record for Presenilin 1 (PSEN1) Associated LocusLink record External resources Additional info in OMIM Content s Each record provides a state of the art summary of current knowledge Extensive references to literature

39. OMIM Search Results by Titles alzheimer AND presenilin 1

40. Entrez Genome: Gene Location View of chromoso me 14 Gene Name Multiple Maps STSs, ESTs, etc.

41. Entrez Genomes Map Viewer Chromosome 7 GenBank Map Contig Map STS Map Integrated View of Chromosome 7 Multiple Maps STSs, ESTs, etc.

42. Entrez Genome: Gene Location View of chromoso me 14 Gene Name

43. Entrez Genome: Gene Location Entrez Genomes Map Viewer Chromosome 14 Cytogenetic map Location of PSEN1 and surrounding genes

44. Books is… searchable resource of on-line books Page 26

45. TaxBrowser is… browser for the major divisions of living organisms (archaea, bacteria, eukaryota, viruses) taxonomy information such as genetic codes molecular data on extinct organisms Page 26

46. Structure site includes… Molecular Modelling Database (MMDB) biopolymer structures obtained from the Protein Data Bank (PDB) Cn3D (a 3D-structure viewer) vector alignment search tool (VAST) Page 26

47. PDB Protein DataBase –Protein and NA 3D structures –Sequence present –YAFFF

48. HEADER LEUCINE ZIPPER 15-JUL-93 1DGC 1DGC 2 COMPND GCN4 LEUCINE ZIPPER COMPLEXED WITH SPECIFIC 1DGC 3 COMPND 2 ATF/CREB SITE DNA 1DGC 4 SOURCE GCN4: YEAST (SACCHAROMYCES CEREVISIAE); DNA: SYNTHETIC 1DGC 5 AUTHOR T.J.RICHMOND 1DGC 6 REVDAT 1 22-JUN-94 1DGC 0 1DGC 7 JRNL AUTH P.KONIG,T.J.RICHMOND 1DGC 8 JRNL TITL THE X-RAY STRUCTURE OF THE GCN4-BZIP BOUND TO 1DGC 9 JRNL TITL 2 ATF/CREB SITE DNA SHOWS THE COMPLEX DEPENDS ON DNA 1DGC 10 JRNL TITL 3 FLEXIBILITY 1DGC 11 JRNL REF J.MOL.BIOL. V. 233 139 1993 1DGC 12 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 0070 1DGC 13 REMARK 1 1DGC 14 REMARK 2 1DGC 15 REMARK 2 RESOLUTION. 3.0 ANGSTROMS. 1DGC 16 REMARK 3 1DGC 17 REMARK 3 REFINEMENT. 1DGC 18 REMARK 3 PROGRAM X-PLOR 1DGC 19 REMARK 3 AUTHORS BRUNGER 1DGC 20 REMARK 3 R VALUE 0.216 1DGC 21 REMARK 3 RMSD BOND DISTANCES 0.020 ANGSTROMS 1DGC 22 REMARK 3 RMSD BOND ANGLES 3.86 DEGREES 1DGC 23 REMARK 3 1DGC 24 REMARK 3 NUMBER OF REFLECTIONS 3296 1DGC 25 REMARK 3 RESOLUTION RANGE 10.0 - 3.0 ANGSTROMS 1DGC 26 REMARK 3 DATA CUTOFF 3.0 SIGMA(F) 1DGC 27 REMARK 3 PERCENT COMPLETION 98.2 1DGC 28 REMARK 3 1DGC 29 REMARK 3 NUMBER OF PROTEIN ATOMS 456 1DGC 30 REMARK 3 NUMBER OF NUCLEIC ACID ATOMS 386 1DGC 31 REMARK 4 1DGC 32 REMARK 4 GCN4: TRANSCRIPTIONAL ACTIVATOR OF GENES ENCODING FOR AMINO 1DGC 33 REMARK 4 ACID BIOSYNTHETIC ENZYMES. 1DGC 34 REMARK 5 1DGC 35 REMARK 5 AMINO ACIDS NUMBERING (RESIDUE NUMBER) CORRESPONDS TO THE 1DGC 36 REMARK 5 281 AMINO ACIDS OF INTACT GCN4. 1DGC 37 REMARK 6 1DGC 38 REMARK 6 BZIP SEQUENCE 220 - 281 USED FOR CRYSTALLIZATION. 1DGC 39 REMARK 7 1DGC 40 REMARK 7 MODEL FROM AMINO ACIDS 227 - 281 SINCE AMINO ACIDS 220 - 1DGC 41 REMARK 7 226 ARE NOT WELL ORDERED. 1DGC 42 REMARK 8 1DGC 43 REMARK 8 RESIDUE NUMBERING OF NUCLEOTIDES: 1DGC 44 REMARK 8 5' T G G A G A T G A C G T C A T C T C C 1DGC 45 REMARK 8 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 1 2 3 4 5 6 7 8 9 1DGC 46 REMARK 9 1DGC 47 REMARK 9 THE ASYMMETRIC UNIT CONTAINS ONE HALF OF PROTEIN/DNA 1DGC 48 REMARK 9 COMPLEX PER ASYMMETRIC UNIT. 1DGC 49 REMARK 10 1DGC 50 REMARK 10 MOLECULAR DYAD AXIS OF PROTEIN DIMER AND PALINDROMIC HALF 1DGC 51 REMARK 10 SITES OF THE DNA COINCIDES WITH CRYSTALLOGRAPHIC TWO-FOLD 1DGC 52 REMARK 10 AXIS. THE FULL PROTEIN/DNA COMPLEX CAN BE OBTAINED BY 1DGC 53 REMARK 10 APPLYING THE FOLLOWING TRANSFORMATION MATRIX AND 1DGC 54 REMARK 10 TRANSLATION VECTOR TO THE COORDINATES X Y Z: 1DGC 55 REMARK 10 1DGC 56 REMARK 10 0 -1 0 X 117.32 X SYMM 1DGC 57 REMARK 10 -1 0 0 Y + 117.32 = Y SYMM 1DGC 58 REMARK 10 0 0 -1 Z 43.33 Z SYMM 1DGC 59 SEQRES 1 A 62 ILE VAL PRO GLU SER SER ASP PRO ALA ALA LEU LYS ARG 1DGC 60 SEQRES 2 A 62 ALA ARG ASN THR GLU ALA ALA ARG ARG SER ARG ALA ARG 1DGC 61 SEQRES 3 A 62 LYS LEU GLN ARG MET LYS GLN LEU GLU ASP LYS VAL GLU 1DGC 62 SEQRES 4 A 62 GLU LEU LEU SER LYS ASN TYR HIS LEU GLU ASN GLU VAL 1DGC 63 SEQRES 5 A 62 ALA ARG LEU LYS LYS LEU VAL GLY GLU ARG 1DGC 64 SEQRES 1 B 19 T G G A G A T G A C G T C 1DGC 65 SEQRES 2 B 19 A T C T C C 1DGC 66 HELIX 1 A ALA A 228 LYS A 276 1 1DGC 67 CRYST1 58.660 58.660 86.660 90.00 90.00 90.00 P 41 21 2 8 1DGC 68 ORIGX1 1.000000 0.000000 0.000000 0.00000 1DGC 69 ORIGX2 0.000000 1.000000 0.000000 0.00000 1DGC 70 ORIGX3 0.000000 0.000000 1.000000 0.00000 1DGC 71 SCALE1 0.017047 0.000000 0.000000 0.00000 1DGC 72 SCALE2 0.000000 0.017047 0.000000 0.00000 1DGC 73 SCALE3 0.000000 0.000000 0.011539 0.00000 1DGC 74 ATOM 1 N PRO A 227 35.313 108.011 15.140 1.00 38.94 1DGC 75 ATOM 2 CA PRO A 227 34.172 107.658 15.972 1.00 39.82 1DGC 76 ATOM 842 C5 C B 9 57.692 100.286 22.744 1.00 29.82 1DGC 916 ATOM 843 C6 C B 9 58.128 100.193 21.465 1.00 30.63 1DGC 917 TER 844 C B 9 1DGC 918 MASTER 46 0 0 1 0 0 0 6 842 2 0 7 1DGC 919 END 1DGC 920 PDB HEADER COMPND SOURCE AUTHOR DATE JRNL REMARK SECRES ATOM COORDINATES

49. Accessing information on molecular sequences Page 26

50. Accession numbers are labels for sequences NCBI includes databases (such as GenBank) that contain information on DNA, RNA, or protein sequences. You may want to acquire information beginning with a query such as the name of a protein of interest, or the raw nucleotides comprising a DNA sequence of interest. DNA sequences and other molecular data are tagged with accession numbers that are used to identify a sequence or other record relevant to molecular data. Page 26

51. What is an accession number? An accession number is label that used to identify a sequence. It is a string of letters and/or numbers that corresponds to a molecular sequence. Examples (all for retinol-binding protein, RBP4): X02775GenBank genomic DNA sequence NT_030059Genomic contig Rs7079946dbSNP (single nucleotide polymorphism) N91759.1An expressed sequence tag (1 of 170) NM_006744RefSeq DNA sequence (from a transcript) NP_007635RefSeq protein AAC02945GenBank protein Q28369SwissProt protein 1KT7Protein Data Bank structure record protein DNA RNA Page 27

52. Four ways to access DNA and protein sequences [1] Entrez Gene with RefSeq [2] UniGene [3] European Bioinformatics Institute (EBI) and Ensembl (separate from NCBI) [4] ExPASy Sequence Retrieval System (separate from NCBI) Page 27 Note: LocusLink at NCBI was recently retired. The third printing of the book has updated these sections (pages 27-31).

53. 4 ways to access protein and DNA sequences [1] Entrez Gene with RefSeq Entrez Gene is a great starting point: it collects key information on each gene/protein from major databases. It covers all major organisms. RefSeq provides a curated, optimal accession number for each DNA (NM_006744) or protein (NP_007635) Page 27

54. From the NCBI home page, type “rbp4” and hit “Go” Pevsner Fig. 2.7 Page 29

55. revised Fig. 2.7 Page 29

59. By applying limits, there are now just two entries

60. [ rest of protein sequence deleted for brevity] [rest of nucleotide sequence deleted for brevity] GenBank Record Accession Number gi Number Protein Sequence Nucleotide Sequence Locus Name Medline ID GenPept ID

61. LOCUS, Accession, NID and protein_id LOCUS: Unique string of 10 letters and numbers in the database. Not maintained amongst databases, and is therefore a poor sequence identifier. ACCESSION: A unique identifier to that record, citable entity; does not change when record is updated. A good record identifier, ideal for citation in publication. VERSION: : New system where the accession and version play the same function as the accession and gi number. Nucleotide gi: Geninfo identifier (gi), a unique integer which will change every time the sequence changes. PID: Protein Identifier: g, e or d prefix to gi number. Can have one or two on one CDS. Protein gi: Geninfo identifier (gi), a unique integer which will change every time the sequence changes. protein_id: Identifier which has the same structure and function as the nucleotide Accession.version numbers, but slightlt different format.

62. revised Fig. 2.8 Page 30 Entrez Gene (top of page) Note that links to many other RBP4 database entries are available

63. Entrez Gene (middle of page)

64. Entrez Gene (bottom of page)

65. Fig. 2.9 Page 32

66. Fig. 2.9 Page 32

67. Fig. 2.9 Page 32

69. FASTA format Fig. 2.10 Page 32

70. What is an accession number? An accession number is label that used to identify a sequence. It is a string of letters and/or numbers that corresponds to a molecular sequence. Examples (all for retinol-binding protein, RBP4): X02775GenBank genomic DNA sequence NT_030059Genomic contig Rs7079946dbSNP (single nucleotide polymorphism) N91759.1An expressed sequence tag (1 of 170) NM_006744RefSeq DNA sequence (from a transcript) NP_007635RefSeq protein AAC02945GenBank protein Q28369SwissProt protein 1KT7Protein Data Bank structure record protein DNA RNA Page 27

71. NCBI’s important RefSeq project: best representative sequences RefSeq (accessible via the main page of NCBI) provides an expertly curated accession number that corresponds to the most stable, agreed-upon “reference” version of a sequence. RefSeq identifiers include the following formats: Complete genomeNG_###### Complete chromosomeNC_###### Genomic contigNT_###### mRNA (DNA format)NM_###### e.g. NM_006744 ProteinNP_###### e.g. NP_006735 Page 29-30

72. Accession MoleculeMethodNote AC_123456 GenomicMixedAlternate complete genomic AP_123456 ProteinMixedProtein products; alternate NC_123456 GenomicMixedComplete genomic molecules NG_123456 GenomicMixedIncomplete genomic regions NM_123456 mRNAMixedTranscript products; mRNA NM_123456789 mRNAMixedTranscript products; 9-digit NP_123456 ProteinMixedProtein products; NP_123456789 ProteinCurationProtein products; 9-digit NR_123456 RNAMixedNon-coding transcripts NT_123456 GenomicAutomatedGenomic assemblies NW_123456 GenomicAutomatedGenomic assemblies NZ_ABCD12345678 GenomicAutomatedWhole genome shotgun data XM_123456 mRNAAutomatedTranscript products XP_123456 ProteinAutomatedProtein products XR_123456 RNAAutomatedTranscript products YP_123456 ProteinAuto. & CuratedProtein products ZP_12345678 ProteinAutomatedProtein products NCBI’s RefSeq project: accession for genomic, mRNA, protein sequences

73. Four ways to access DNA and protein sequences [1] Entrez Gene with RefSeq [2] UniGene [3] European Bioinformatics Institute (EBI) and Ensembl (separate from NCBI) [4] ExPASy Sequence Retrieval System (separate from NCBI) Page 31

74. DNARNA complementary DNA (cDNA) protein UniGene Fig. 2.3 Page 23 In genetics, complementary DNA (cDNA) is DNA synthesized from a mature mRNA template in a reaction catalyzed by the enzyme reverse transcriptase.geneticsDNAmRNAreverse transcriptase

75. Expressed Sequence Tag What Are ESTs and How Are They Made? ESTs are small pieces of DNA sequence (usually 200 to 500 nucleotides long) that are generated by sequencing either one or both ends of an expressed gene. The idea is to sequence bits of DNA that represent genes expressed in certain cells, tissues, or organs from different organisms and use these "tags" to fish a gene out of a portion of chromosomal DNA by matching base pairs. The challenge associated with identifying genes from genomic sequences varies among organisms and is dependent upon genome size as well as the presence or absence of introns, the intervening DNA sequences interrupting the protein coding sequence of a gene.

76. STS Sequenced Tagged Sites, are operationally unique sequence that identifies the combination of primer pairs used in a PCR assay that generate a mapping reagent which maps to a single position within the genome. Also see: http://www.ncbi.nlm.nih.gov/dbSTS/ http://www.ncbi.nlm.nih.gov/genemap/

77. UniGene: unique genes via ESTs Find UniGene at NCBI: www.ncbi.nlm.nih.gov/UniGene UniGene clusters contain many expressed sequence tags (ESTs), which are DNA sequences (typically 500 base pairs in length) corresponding to the mRNA from an expressed gene. ESTs are sequenced from a complementary DNA (cDNA) library. UniGene data come from many cDNA libraries. Thus, when you look up a gene in UniGene you get information on its abundance and its regional distribution. Pages 20-21

78. Cluster sizes in UniGene This is a gene with 1 EST associated; the cluster size is 1 Fig. 2.3 Page 23

79. Cluster sizes in UniGene This is a gene with 10 ESTs associated; the cluster size is 10

80. Cluster sizes in UniGene (human) Cluster size (ESTs) Number of clusters 1  42,800 26,500 3-46,500 5-85,400 9-164,100 17-323,300  500-10002,128  2000-4000233  8000-16,00021  16,000-30,0008 UniGene build 194, 8/06

81. UniGene: unique genes via ESTs Conclusion: UniGene is a useful tool to look up information about expressed genes. UniGene displays information about the abundance of a transcript (expressed gene), as well as its regional distribution of expression (e.g. brain vs. liver). We will discuss UniGene further later (gene expression). Page 31

82. Five ways to access DNA and protein sequences [1] Entrez Gene with RefSeq [2] UniGene [3] European Bioinformatics Institute (EBI) and Ensembl (separate from NCBI) [4] ExPASy Sequence Retrieval System (separate from NCBI) Page 31

83. Ensembl to access protein and DNA sequences Try Ensembl at www.ensembl.org for a premier human genome web browser. We will encounter Ensembl as we study the human genome, BLAST, and other topics.

84. click human

85. enter RBP4

87. Five ways to access DNA and protein sequences [1] Entrez Gene with RefSeq [2] UniGene [3] European Bioinformatics Institute (EBI) and Ensembl (separate from NCBI) [4] ExPASy Sequence Retrieval System (separate from NCBI) Page 33

88. ExPASy to access protein and DNA sequences ExPASy sequence retrieval system (ExPASy = Expert Protein Analysis System) Visit http://www.expasy.ch/ Page 33

89. Fig. 2.11 Page 33

91. Example of how to access sequence data: HIV-1 pol There are many possible approaches. Begin at the main page of NCBI, and type an Entrez query: hiv-1 pol Page 34

93. Searching for HIV-1 pol: Following the “genome” link yields a manageable three results

94. Example of how to access sequence data: HIV-1 pol For the Entrez query: hiv-1 pol there are about 40,000 nucleotide or protein records (and >100,000 records for a search for “hiv-1”), but these can easily be reduced in two easy steps: --specify the organism, e.g. hiv-1[organism] --limit the output to RefSeq! Page 34

95. only 1 RefSeq over 100,000 nucleotide entries for HIV-1

96. Examples of how to access sequence data: histone query for “histone”# results protein records21847 RefSeq entries7544 RefSeq (limit to human)1108 NOT deacetylase697 At this point, select a reasonable candidate (e.g. histone 2, H4) and follow its link to Entrez Gene. There, you can confirm you have the right gene/protein. 8-12-06

98. Access to Biomedical Literature Page 35

99. PubMed at NCBI to find literature information

100. PubMed is the NCBI gateway to MEDLINE. MEDLINE contains bibliographic citations and author abstracts from over 4,600 journals published in the United States and in 70 foreign countries. It has >14 million records dating back to 1966. Page 35

101. MeSH is the acronym for "Medical Subject Headings." MeSH is the list of the vocabulary terms used for subject analysis of biomedical literature at NLM. MeSH vocabulary is used for indexing journal articles for MEDLINE. The MeSH controlled vocabulary imposes uniformity and consistency to the indexing of biomedical literature. Page 35

104. PubMed search strategies Try the tutorial (“education” on the left sidebar) Use boolean queries (capitalize AND, OR, NOT) lipocalin AND disease Try using “limits” Try “Links” to find Entrez information and external resources Obtain articles on-line via Welch Medical Library (and download pdf files): http://www.welch.jhu.edu/ Page 35

105. lipocalin AND disease (60 results) lipocalin OR disease (1,650,000 results) lipocalin NOT disease (530 results) 1 AND 2 1 OR 2 1 NOT 2 1 1 1 2 2 2 Fig. 2.12 Page 34 8/04

106. true positive “globin” is found 8/06 “globin” is not found “globin” is present “globin” is absent Article contents: Search result: true negative false negative ( article discusses globins ) false positive ( article does not discuss globins )

111. Protein sequence motif is a descriptor of a protein family Glutamine amidotransferase class I [PAS]-[LIVMFYT]-[LIVMFY]-G-[LIVMFY]-C- [LIVMFYN]-G-x-[QEH]- x-[LIVMFA] [C is the active site residue] Glutamine amidotransferase class II <x(0,11)-C-[GS]-[IV]-[LIVMFYW]-[AG] [C is the active site residue]

117. Searching MMDB

118. Principles of structural alignment Dali: http://www.ebi.ac.uk/dali/ Looks for minimal RMSD between C  atoms. Calculate C  - C  distance matrices, then identifies the longest alignable segments VAST (Vector Alignment Search Tool) http://www.ncbi.nlm.nih.gov/Structure/ looks for pairs of secondary structure elements (  -helices,  -strands) that have similar orientation and connectivity

119. Dali alignment of Tyr phosphatase

120. VAST Structure Neighbors

121. Structure Summary Cn3D viewer VAST neighbors BLAST neighbors

122. Cn3D : Displaying Structures Chloroquine

123. Structure Neighbors

124. Use of structural alignments Chloroquine NADH

125. PDB Protein DataBase –Protein and NA 3D structures –Sequence present –YAFFF

126. HEADER LEUCINE ZIPPER 15-JUL-93 1DGC 1DGC 2 COMPND GCN4 LEUCINE ZIPPER COMPLEXED WITH SPECIFIC 1DGC 3 COMPND 2 ATF/CREB SITE DNA 1DGC 4 SOURCE GCN4: YEAST (SACCHAROMYCES CEREVISIAE); DNA: SYNTHETIC 1DGC 5 AUTHOR T.J.RICHMOND 1DGC 6 REVDAT 1 22-JUN-94 1DGC 0 1DGC 7 JRNL AUTH P.KONIG,T.J.RICHMOND 1DGC 8 JRNL TITL THE X-RAY STRUCTURE OF THE GCN4-BZIP BOUND TO 1DGC 9 JRNL TITL 2 ATF/CREB SITE DNA SHOWS THE COMPLEX DEPENDS ON DNA 1DGC 10 JRNL TITL 3 FLEXIBILITY 1DGC 11 JRNL REF J.MOL.BIOL. V. 233 139 1993 1DGC 12 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 0070 1DGC 13 REMARK 1 1DGC 14 REMARK 2 1DGC 15 REMARK 2 RESOLUTION. 3.0 ANGSTROMS. 1DGC 16 REMARK 3 1DGC 17 REMARK 3 REFINEMENT. 1DGC 18 REMARK 3 PROGRAM X-PLOR 1DGC 19 REMARK 3 AUTHORS BRUNGER 1DGC 20 REMARK 3 R VALUE 0.216 1DGC 21 REMARK 3 RMSD BOND DISTANCES 0.020 ANGSTROMS 1DGC 22 REMARK 3 RMSD BOND ANGLES 3.86 DEGREES 1DGC 23 REMARK 3 1DGC 24 REMARK 3 NUMBER OF REFLECTIONS 3296 1DGC 25 REMARK 3 RESOLUTION RANGE 10.0 - 3.0 ANGSTROMS 1DGC 26 REMARK 3 DATA CUTOFF 3.0 SIGMA(F) 1DGC 27 REMARK 3 PERCENT COMPLETION 98.2 1DGC 28 REMARK 3 1DGC 29 REMARK 3 NUMBER OF PROTEIN ATOMS 456 1DGC 30 REMARK 3 NUMBER OF NUCLEIC ACID ATOMS 386 1DGC 31 REMARK 4 1DGC 32 REMARK 4 GCN4: TRANSCRIPTIONAL ACTIVATOR OF GENES ENCODING FOR AMINO 1DGC 33 REMARK 4 ACID BIOSYNTHETIC ENZYMES. 1DGC 34 REMARK 5 1DGC 35 REMARK 5 AMINO ACIDS NUMBERING (RESIDUE NUMBER) CORRESPONDS TO THE 1DGC 36 REMARK 5 281 AMINO ACIDS OF INTACT GCN4. 1DGC 37 REMARK 6 1DGC 38 REMARK 6 BZIP SEQUENCE 220 - 281 USED FOR CRYSTALLIZATION. 1DGC 39 REMARK 7 1DGC 40 REMARK 7 MODEL FROM AMINO ACIDS 227 - 281 SINCE AMINO ACIDS 220 - 1DGC 41 REMARK 7 226 ARE NOT WELL ORDERED. 1DGC 42 REMARK 8 1DGC 43 REMARK 8 RESIDUE NUMBERING OF NUCLEOTIDES: 1DGC 44 REMARK 8 5' T G G A G A T G A C G T C A T C T C C 1DGC 45 REMARK 8 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 1 2 3 4 5 6 7 8 9 1DGC 46 REMARK 9 1DGC 47 REMARK 9 THE ASYMMETRIC UNIT CONTAINS ONE HALF OF PROTEIN/DNA 1DGC 48 REMARK 9 COMPLEX PER ASYMMETRIC UNIT. 1DGC 49 REMARK 10 1DGC 50 REMARK 10 MOLECULAR DYAD AXIS OF PROTEIN DIMER AND PALINDROMIC HALF 1DGC 51 REMARK 10 SITES OF THE DNA COINCIDES WITH CRYSTALLOGRAPHIC TWO-FOLD 1DGC 52 REMARK 10 AXIS. THE FULL PROTEIN/DNA COMPLEX CAN BE OBTAINED BY 1DGC 53 REMARK 10 APPLYING THE FOLLOWING TRANSFORMATION MATRIX AND 1DGC 54 REMARK 10 TRANSLATION VECTOR TO THE COORDINATES X Y Z: 1DGC 55 REMARK 10 1DGC 56 REMARK 10 0 -1 0 X 117.32 X SYMM 1DGC 57 REMARK 10 -1 0 0 Y + 117.32 = Y SYMM 1DGC 58 REMARK 10 0 0 -1 Z 43.33 Z SYMM 1DGC 59 SEQRES 1 A 62 ILE VAL PRO GLU SER SER ASP PRO ALA ALA LEU LYS ARG 1DGC 60 SEQRES 2 A 62 ALA ARG ASN THR GLU ALA ALA ARG ARG SER ARG ALA ARG 1DGC 61 SEQRES 3 A 62 LYS LEU GLN ARG MET LYS GLN LEU GLU ASP LYS VAL GLU 1DGC 62 SEQRES 4 A 62 GLU LEU LEU SER LYS ASN TYR HIS LEU GLU ASN GLU VAL 1DGC 63 SEQRES 5 A 62 ALA ARG LEU LYS LYS LEU VAL GLY GLU ARG 1DGC 64 SEQRES 1 B 19 T G G A G A T G A C G T C 1DGC 65 SEQRES 2 B 19 A T C T C C 1DGC 66 HELIX 1 A ALA A 228 LYS A 276 1 1DGC 67 CRYST1 58.660 58.660 86.660 90.00 90.00 90.00 P 41 21 2 8 1DGC 68 ORIGX1 1.000000 0.000000 0.000000 0.00000 1DGC 69 ORIGX2 0.000000 1.000000 0.000000 0.00000 1DGC 70 ORIGX3 0.000000 0.000000 1.000000 0.00000 1DGC 71 SCALE1 0.017047 0.000000 0.000000 0.00000 1DGC 72 SCALE2 0.000000 0.017047 0.000000 0.00000 1DGC 73 SCALE3 0.000000 0.000000 0.011539 0.00000 1DGC 74 ATOM 1 N PRO A 227 35.313 108.011 15.140 1.00 38.94 1DGC 75 ATOM 2 CA PRO A 227 34.172 107.658 15.972 1.00 39.82 1DGC 76 ATOM 842 C5 C B 9 57.692 100.286 22.744 1.00 29.82 1DGC 916 ATOM 843 C6 C B 9 58.128 100.193 21.465 1.00 30.63 1DGC 917 TER 844 C B 9 1DGC 918 MASTER 46 0 0 1 0 0 0 6 842 2 0 7 1DGC 919 END 1DGC 920 PDB HEADER COMPND SOURCE AUTHOR DATE JRNL REMARK SECRES ATOM COORDINATES

127. UniProt New protein sequence database that is the result of a merge from SWISS-PROT and PIR. It will be the annotated curated protein sequence database. Data in UniProt is primarily derived from coding sequence annotations in EMBL (GenBank/DDBJ) nucleic acid sequence data. UniProt is a Flat-File database just like EMBL and GenBank Flat-File format is SwissProt-like, or EMBL-like

128. Swiss-Prot

129. SWISS-PROT incorporates: Function of the protein Post-translational modification Domains and sites. Secondary structure. Quaternary structure. Similarities to other proteins; Diseases associated with deficiencies in the protein Sequence conflicts, variants, etc. Swiss-Prot SWISS-PROT incorporates: Function of the protein Post-translational modification Domains and sites. Secondary structure. Quaternary structure. Similarities to other proteins; Diseases associated with deficiencies in the protein Sequence conflicts, variants, etc.