1. Molecular biology databases
Based on Chapter 2 of
Post-genome Informatics by Minoru Kanehisa, Oxford University Press, 2000
2.1 History
2.2 Information Technology
2.3 New generation databases

2. Evolution of molecular biology databases

3. The addresses for the major databases

4. New generation of molecular biology databases

7. Example of sequence database entry for Genbank
LOCUS DRODPPC 4001 bp INV 15-MAR-1990
DEFINITION D.melanogaster decapentaplegic gene complex (DPP-C), complete cds.
ACCESSION M30116
KEYWORDS .
SOURCE D.melanogaster, cDNA to mRNA.
ORGANISM Drosophila melanogaster
Eurkaryote; mitochondrial eukaryotes; Metazoa; Arthropoda;
Tracheata; Insecta; Pterygota; Diptera; Brachycera; Muscomorpha;
Ephydroidea; Drosophilidae; Drosophilia.
REFERENCE 1 (bases 1 to 4001)
AUTHORS Padgett, R.W., St Johnston, R.D. and Gelbart, W.M.
TITLE A transcript from a Drosophila pattern gene predicts a protein
homologous to the transforming growth factor-beta family
JOURNAL Nature 325, (1987)
MEDLINE
COMMENT The initiation codon could be at either or
FEATURES Location/Qualifiers
source
/organism=“Drosophila melanogaster”
/db_xref=“taxon:7227”
mRNA <
/gene=“dpp”
/note=“decapentaplegic protein mRNA”
/db_xref=“FlyBase:FBgn ”
gene
/note=“decapentaplegic”
/allele=“”
CDS
/note=“decapentaplegic protein (1188 could be 1587)”
/codon_start=1
/db_xref=“PID:g157292”
/translation=“MRAWLLLLAVLATFQTIVRVASTEDISQRFIAAIAPVAAHIPLA
SASGSGSGRSGSRSVGASTSTALAKAFNPFSEPASFSDSDKSHRSKTNKKPSKSDANR
……………………
LGYDAYYCHGKCPFPLADHFNSTNAVVQTLVNNMNPGKVPKACCVPTQLDSVAMLYL
NDQSTBVVLKNYQEMTBBGCGCR”
BASE COUNT 1170 a 1078 c 956 g 797 t
ORIGIN
1 gtcgttcaac agcgctgatc gagtttaaat ctataccgaa atgagcggcg gaaagtgagc
61 cacttggcgt gaacccaaag ctttcgagga aaattctcgg acccccatat acaaatatcg
121 gaaaaagtat cgaacagttt cgcgacgcga agcgttaaga tcgcccaaag atctccgtgc
181 ggaaacaaag aaattgaggc actattaaga gattgttgtt gtgcgcgagt gtgtgtcttc
241 agctgggtgt gtggaatgtc aactgacggg ttgtaaaggg aaaccctgaa atccgaacgg
301 ccagccaaag caaataaagc tgtgaatacg aattaagtac aacaaacagt tactgaaaca
361 gatacagatt cggattcgaa tagagaaaca gatactggag atgcccccag aaacaattca
421 attgcaaata tagtgcgttg cgcgagtgcc agtggaaaaa tatgtggatt acctgcgaac
481 cgtccgccca aggagccgcc gggtgacagg tgtatccccc aggataccaa cccgagccca
541 gaccgagatc cacatccaga tcccgaccgc agggtgccag tgtgtcatgt gccgcggcat
601 accgaccgca gccacatcta ccgaccaggt gcgcctcgaa tgcggcaaca caattttcaa
………………………….
3841 aactgtataa acaaaacgta tgccctataa atatatgaat aactatctac atcgttatgc
3901 gttctaagct aagctcgaat aaatccgtac acgttaatta atctagaatc gtaagaccta
3961 acgcgtaagc tcagcatgtt ggataaatta atagaaacga g //

8. Example of sequence database entry for SWISS-PROT
ID DECA_DROME STANDARD; PRT; 588AA.
AC P07713;
DT 01-APR-1988 (REL. 07, CREATED)
DT 01-APR-1988 (REL. 07, LAST SEQUENCE UPDATE)
DT 01-FEB-1995 (REL. 31, LAST ANNOTATION UPDATE)
DE DECAPENTAPLEGIC PROTEIN PRECURSOR (DPP-C PROTEIN).
GN DPP.
OS DROSOPHILA MELANOGASTER (FRUIT FLY).
OC EUKARYOTA; METAZOA; ARTHROPODA; INSECTA; DIPTERA.
RN [1]
RP SEQUENCE FROM N.A. RM
RA PADGETT R.W., ST JOHNSTON R.D., GELBART W.M.;
RL NATURE 325:81-84 (1987)
RN [2]
RP CHARACTERIZATION, AND SEQUENCE OF RM
RA PANGANIBAN G.E.F., RASHKA K.E., NEITZEL M.D., HOFFMANN F.M.;
RL MOL. CELL. BIOL. 10: (1990).
CC -!- FUNCTION: DPP IS REQUIRED FOR THE PROPER DEVELOPMENT OF THE
CC EMBRYONIC DOORSAL HYPODERM, FOR VIABILITY OF LARVAE AND FOR CELL
CC VIABILITY OF THE EPITHELIAL CELLS IN THE IMAGINAL DISKS.
CC -!- SUBUNIT: HOMODIMER, DISULFIDE-LINKED.
CC -!- SIMILARITY: TO OTHER GROWTH FACTORS OF THE TGF-BETA FAMILY.
DR EMBL; M30116; DMDPPC.
DR PIR; A26158; A26158.
DR HSSP; P08112; 1TFG.
DR FLYBASE; FBGN ; DPP.
DR PROSITE; PS00250; TGF_BETA.
KW GROWTH FACTOR; DIFFERENTIATION; SIGNAL.
FT SIGNAL 1 ? POTENTIAL.
FT PROPEP ? 456
FT CHAIN DECAPENTAPLEGIC PROTEIN.
FT DISULFID BY SIMILARITY.
FT DISULFID BY SIMILARITY.
FT DISULFID BY SIMILARITY.
FT DISULFID INTERCHAIN (BY SIMILARITY).
FT CARBOHYD POTENTIAL.
FT CARBOHYD POTENTIAL.
FT CARBOHYD POTENTIAL.
FT CARBOHYD POTENTIAL.
SQ SEQUENCE AA; MW; CN;
MRAWLLLLAV LATFQTIVRV ASTEDISQRF IAAIAPVAAH IPLASASGSG SGRSGSRSVG
ASTSTAGAKA FNRFSEPASF SDSDKSHRSK TNKKPSKSDA NRQFNEVHKP RTDQLENSKN
KSKQLVNKPN HNKMAVKEQR SHHKKSHHHR SHQPKQASAS TESHQSSSIE SIFVEEPTLV
LDREVASINV PANAKAIIAE QGPSTYSKEA LIKDKLKPDP STYLVEIKSL LSLFNMKRPP
KIDRSKIIIP EPMKKLYAEI MGHELDSVNI PKPGLLTKSA NTVRSFTHKD SKIDDRFPHH
HRFRLHFDVK SIPADEKLKA AELQLTRDAL SQQVVASRSS ANRTRYQBLV YDITRVGVRG
QREPSYLLLD TKTBRLNSTD TVSLDVQPAV DRWLASPQRN YGLLVEVRTV RSLKPAPHHH
VRLRRSADEA HERWQHKQPL LFTYTDDGRH DARSIRDVSG GEGGGKGGRN KRHARRPTRR
KNHDDTCRRH SLYVDFSDVG WDDWIVAPLG YDAYYCHGKC PFPLADHRNS TNHAVVQTLV
NNMNPGKBPK ACCBPTQLDS VAMLYLNDQS TVVLKNYQEM TVVGCGCR

9. Functional classification of E. coli genes according to Monica Riley

10. Relational database. A table (relation) is a set and the three basic table operations shown here are extensions of the standard set operations.
MUID
Journal
Volume
Pages
Year
Paper 1
Paper 2
Paper 3
Paper 4
SELECT
PROJECT
MUID
Journal
Volume
Pages
Author
Year
Author
JOIN
MUID
Author 1-1
Author 1-2
Author 2-1
Author 2-2
Author 2-3
Author 3-1

13. A history of database technology development
Relational database
(Codd, 1970)
Object-oriented
Programming
(Kay, 1972)
Logic programming
(Kowalski, 1972)
Object-oriented
Database
(1986)
Deductive database\
(1977)
Deductive, object-
Oriented database
(1989)

15. Multimedia in GenomeNet

17. Pancreatic trypsin inhibitor PDB: 4PTI
ribbon model and variant with cylinder
for alpha helix (figures from PDB)

19. The periodic table of chemical elements where the shaded elements are those normally found in biology.

20. Biologically important classes of organic compounds derived from the six basic elements

21. The 20 common
amino acids

22. BLO(ck)SU(bstitution)M(atrix) (Henikoff & Henikoff 1992)
Derived from a set (2000) of aligned and ungapped regions from protein families; emphasizing more on chemical similarities (versus how easy it is to mutate from one residue to another). BLOSUMx is derived from the set of segments of x% identity.
BLOSUM62 Matrix, log-odds representation

23. Substitution/Scoring Matrices
Pam matrices (Dayhoff et al. 1978) --- phylogeny-based.
PAM1: expected number of mutation = 1%
PAM250 matrix, log-odds representation

25. A hidden Markov model for sequence analysis
Start
End
m= match state (output), I = insert state (output), d= delete state (no output)

27. Globin fold
 protein
myoglobin
PDB: 1MBN

28.  sandwich
 protein
immunoglobulin
PDB: 7FAB

29. TIM barrel
 /  protein
Triose
phosphate
IsoMerase
PDB: 1TIM

30. A fold in
 + protein
ribonuclease A
PDB: 7RSA

32. 434 Cro
protein
complex
(phage)
PDB: 3CRO

33. ..YRCKVCSRVY THISNFCRHY VTSH...
Zinc finger
DNA recognition
(Drosophila)
PDB: 2DRP
..YRCKVCSRVY THISNFCRHY VTSH...

34. ..RA RKLQRMKQLE DKVEE LLSKN YHLENEVARL...
Leucine zipper
(yeast)
PDB: 1YSA
..RA RKLQRMKQLE DKVEE LLSKN YHLENEVARL...

35. The orthologue group table for F1-F0 ATP synthase (upper) and V-type ATP synthase (lower).

37. Note notion of Enzyme Commission (EC) number.
Reactions and interactions
Note notion of Enzyme Commission (EC) number.
Biochemical pathways
Genome diversity

38. The tree of life showing the relationship of archaea, bacteria, and eukaryotes, as well as the relationship of fungi, plants and animals.
Animals
Fungi
Plants
Protists
Eukaryotes
Archae
Bacteria