512 3 4 5

1 2 3 4 56

1EMBL http://www.embl-heidelberg.de 2GenBank http://www.ncbi.nlm.nih.gov/Web/Genbank/index.html 3DDBJ http://www.ddbj.nig.ac.jp/

bp

DNARNADNARNA

EBML

MBLGigabasesEST-Expressed sequence tags; STS-sequence tagged siteshttp://www3.ebi.ac.uk/Services/DBStats/

21 Mar 2003 37,943,364,438 bases in 24,353,128 records.

ID ACXX DT DEKWOGOSOCRNRPRARTRLRCRXDRFH FT 1Feature Key 2Location 3QualifiersSQ//EMBL EMBLASCII annotation

12Authorin3WWW

EMBL1CD-ROM2ftp3Gopher4WWW

EMBL3W1X58929SCARGC

HTML

MEDLINEMEDLINE

:

J00231DRSWISS-PROTP01860GC3_HUMAN2 3WFastAFastA

2GDB GDB1 PCR ESTcontigs 2 contig 3

MGDhttp://www.informatics.jax.org/

SGDhttp://genome-www.stanford.edu/Saccharomyces/

Ensembl (http://www.ensembl.org/3EnsemblEnsemblDNA

GenScan

SNP

Ensembl

Ensembl

BLAST

9

4dbESTESTExpressed Sequence Tags EST90% DbEST (http://www.ncbi.nlm.nih.gov/dbEST/GenBankESTmRNA WEBemailFTPESTdbEST

5dbSTSSTSSequence Tagged Sites

dbSTShttp://www.ncbi.nlm.nih.gov/dbSTS/NCBISTS

BLASTSTS

6UniGeneUniGene( http://www.ncbi.nlm.nih.gov/UniGene/)GenBank UniGene: EST UniGeneEST

99%1PIRProtein Information Resource

PIR (1) (2) (3) (4)

PIR:

BLASTFastA

2SWISS-PROT SWISS-PROT (http://www.expasy.ch/sprot/sprot-top.html, SWISS-PROT12PIR34 SWISS-PROT

1

SWISS-PROT

A) (B) (C)ATP (D) (E) (F) (G) (H)

2 3 EMBL PROSITE PDB

ab) AuthorincWWW

SWISS-PROTaCD-ROMbftpcGopherdWWWSRS

a b

TrEMBL (http://www.ebi.ac.uk/trembl/index.html) SWISS-PROTEMBL(CDS)SWISS-PROT

TrEMBL1SP-TrEMBL(SWISS-PROT TrEMBL)SWISS-PROTSP-TrEMBL SWISS-PROT

2REM-TrEMBL(REMaining TrEMBL)SWISS-PROT

3TrEMBL

Swiss-Prot TrEMBL PIR BLASTFTP 4UniProt

UniProt31UniProt KnowledgebaseUniProt 2UniProt Non-redundant ReferenceUniRef 3UniProt ArchiveUniParc

1PDBProtein Data BankPDBXNMR

explicit sequencePDBSEQRES

(implicit sequence) PDB

HEADER HYDROLASE 19-FEB-97 1ADZ TITLE THE SOLUTION STRUCTURE OF THE SECOND KUNITZ DOMAIN OF TITLE 2 TISSUE FACTOR PATHWAY INHIBITOR, NMR, 30 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: TISSUE FACTOR PATHWAY INHIBITOR; COMPND 8 BIOLOGICAL_UNIT: MONOMER SOURCE MOL_ID: 1; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PFLAG KEYWDS HYDROLASE, INHIBITOR, COAGULATION EXPDTA NMR, 30 STRUCTURES AUTHOR M.J.M.BURGERING,L.P.M.ORBONS REVDAT 1 25-FEB-98 1ADZ 0 JRNL AUTH M.J.BURGERING,L.P.ORBONS,A.VAN DER DOELEN, REMARK 1 REFERENCE 1 REMARK 1 AUTH M.T.STUBBS II REMARK 1 TITL STRUCTURAL ASPECTS OF FACTOR XA INHIBITION REMARK 999 SEQUENCE REMARK 999 1ADZ SWS P10646 1 - 111 NOT IN ATOMS LIST REMARK 999 1ADZ SWS P10646 183 - 304 NOT IN ATOMS LIST REMARK 999 THE FIRST NINE RESIDUES ARE NOT PART OF THE TFPI DOMAIN II REMARK 999 SEQUENCE BUT ARE FROM THE PFLAG PEPTIDE CLONING VECTOR. DBREF 1ADZ 1 71 SWS P10646 TFPI_HUMAN 112 182 SEQADV 1ADZ ASP 1 SWS P10646 ILE 112 ENGINEERED SEQADV 1ADZ TYR 2 SWS P10646 ILE 113 ENGINEERED SEQRES 1 71 ASP TYR LYS ASP ASP ASP ASP LYS LEU LYS PRO ASP PHE SEQRES 2 71 CYS PHE LEU GLU GLU ASP PRO GLY ILE CYS ARG GLY TYR SEQRES 3 71 ILE THR ARG TYR PHE TYR ASN ASN GLN THR LYS GLN CYS SEQRES 4 71 GLU ARG PHE LYS TYR GLY GLY CYS LEU GLY ASN MET ASN SEQRES 5 71 ASN PHE GLU THR LEU GLU GLU CYS LYS ASN ILE CYS GLU SEQRES 6 71 ASP GLY PRO ASN GLY PHE HELIX 1 1 ASP 12 PHE 15 5 4 HELIX 2 2 ASN 34 THR 36 5 3 HELIX 3 3 LEU 57 ILE 63 1 7 SHEET 1 A 2 ARG 29 ASN 33 0 SHEET 2 A 2 GLN 38 PHE 42 -1 N PHE 42 O ARG 29 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 4.5 PDB PDB

RasMol ChemView

2MMDB(Molecular Modeling Database)MMDB NCBIEntrez PDBMMDB

MMDB

SNPsSingle nucleotide polymorphisms

SNPsSNPs 1dbSNPhttp://www3.ncbi.nlm.nih.gov/SNP/)

GTTTGTGATT ACTTTGTAAA AACAGTGTAA TAAGTACTCA CTAAAGGAAA TTTAGAAAAT GATAAGCTTA Aggccgggca tggtgcctca tgcctgtaat cctagcactt tgggaggctg aggtgggtgg atcacctgag ctcaggagtt ccagatcatc ctggacaata tggtgaaacc ctgtctacgc ttaaaatacg R aaattagccg ggcgtggtgg ggcatgcctg tggtctcagc tactttggag actaaggtag aaggatcact tgaatcctgg aggtggaggt tgcagagtga gccaatatcg tgccactgca ctccagccta ggtgacagag gaagactctg tctcaaaaaa aagaaaaTAA GGCCAGACAC GGGGGCTCAT GCTTGTAATC

R=A/G

2SCOPSCOP ( http://scop.mrc-lmb.cam.ac.uk/scop/PDBSCOPPDB: (1) (2) (3)

3DSSPDSSPhttp://www.sander.embl-heidelberg.de/dssp/ PDBDSSP

The DSSP codeH = alpha helix B = residue in isolated beta-bridge E = extended strand, participates in beta ladder G = 3-helix (3/10 helix) I = 5 helix (pi helix) T = hydrogen bonded turn S = bend

4HSSPHSSP(http://www.sander.embl-heidelberg.de/hssp/PDBSWISS-PROT PDBHSSPHSSP

From PDBFrom Swiss-prot

5OMIMOMIM (Online Mendelian Inheritance in Man), OMIMOMIM http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=OMIM

6EPDEPD( http://www.epd.isb-sib.ch/ )EMBL

7TRRDTRRDTRRD TRRD6.01TRRDGENES 2TRRDLCR 3TRRDUNITS 4TRRDSITES 5TRRDFACTORS 6TRRDEXP 7TRRDBIB

8TRANSFACTRANSFAC http://transfac.gbf.de/ TRANSFAC6 1SITE 2GENE 3FACTOR 4CELL 5CLASS 6MATRIX

9BODYMAPBODYMAP (http://bodymap.ims.u-tokyo.ac.jp/3ESTmRNA,

10PROSITEPROSITE ( http://www.expasy.ch/prosite/) PROSITEPROSITE

11DBCatDBCat500DNARNA http://www.infobiogen.fr/services/dbcat/

DBCat

12PubMedPubMedhttp://www.ncbi.nlm.nih.gov/NCBIMEDLINEPre-MEDLINEEntrezPubMed

O(n2)

FastABLAST

FASTAs: t: 1FASTA = 6 6 8 10s -----A-A-T---t: --A-A-T----- 3 5 7 = 3

FASTP

kkk-tupk=12kk

1k

2ks[i]t[j]i-j

1 2 3 4 5 6 7 8 9 10 11 s = H A R F Y A A Q I V L A 2,6,7 F 4 H 1 I 9 L 11 Q 8 R 3 V 10 Y 5 1 2 3 4 5 6 7 8 t = V D M A A Q I A +9 -2 -3 +2 +2 -6 +2 +1 -2 +3 +2 -1-7 -6 -5 -4 -3 -2 -1 0 +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 1 1 2 1 1 4 1 1

12k5PAMst

FastAFastA32FastA3FastA

FastADNADNAFASTXFASTYDNA TFastADNATFASTXTFASTYDNAFASTSTFASTSDNAFASTFTFASTFDNA

FastA

2BLASTBLAST BLASTFastA BLAST

BLASTS:t:

BLASTS

SSS

BLAST

BLAST

1

2

3

w TwTw4Hash table

DNAw2bit4

BLAST

BLAST

4 Vs. 20

DNA

DNA

3VASTVASTNCBIPDBMMDBVASTCn3DWang et al., 2000 http://www.ncbi.nlm.nih.gov/Structure/VAST/

VAST

.EntrezSRS

1EntrezNCBIOMIMPubmedhttp://www.ncbi.nlm.nih.gov/gorf/gorf.html

Entrez4.8

4.8Entrez

2. SRSSRSSequence Retrieval SystemEMBLWEB

SRSEMBLEMBL_NEWSwissProtPIRPrositeReBasePDBNRL_3DEPDE.coli ECDENZYMESEQANALREF80

SRS

3ExPASyExPASy (Expert Protein Analysis Systemhttp://www.expasy.org/) WWW SWISS-PROTTrEMBLPROSITE23SWISS-2DPAGESWISS-3DIMAGE

GCG GCG (Genetics Computer Group)

140

GCG GenBankEMBL GCGPIRSWISS-PROTSP-TrEMBL

1Gap: BestFit: FrameAlign: CompareDotPlot: GapShowProfileGap:

2PileUp: HmmerAlignPlotSimilarityPrettyPrettyBoxMEMEHmmerBuildHmmerCalibrateProfileMakeProfileGapOverlapNoOverlapOldDistances

3LookUp

StringSearch

Names

4BLASTNetBLASTFastASsearchTFastA/TfastX/FastXFrameSearchMotifSearchHmmerSearchProfileSearchProfileSegmentsFindPatternsMotifsWordSearchHmmerPfamSegments

5DNA/RNAMfoldDNARNAPlotFoldMfoldStemLoop

6PAUPSearchPAUPDisplayDistancesDiverge

7GelStartGelEnterGelMergeGelAssembleGelViewGelDisassemble

8TestCodeCodonPreferenceFramesRepeatCompositionCodonFrequencyCorrespond

9MapMapPlotMapSort: PeptideMapPlasmidMapPeptideSort:

10PrimePrimePairMeltTemp

11ProfileScanCoilScanHTHScanSPScanIsoelectric: PepPlotPeptideStructurePlotStructure

12 ReverseShuffle CorruptSampleDataSetGCGToBLAST