1. string{A, T, G, C}sequence

s=ATTGCATATG|s|; ssi 1 i |s|

0empty string

2. substringsubsequence

s=ATGCGGTA; t=TGCGG; st

s=ATGCGGTA; t=TGTA st

interval

s=ATGCGGTACGTATACG; u=CG, s[i, i+1]

3. uw(concatenation),uws = ATGCGGTA; t=TGCGGst = ATGCGGTATGCGGts = TGCGGATGCGGTAs = ATsss= AT AT AT=s3

prefix

s = ATGCGGTAGC; prefix(s,3)=ATG; prefix(s,0) =

s1u, s=tu, tu

suffix

s = ATGCGGTAGC

suffix(s,3) =AGC suffix(s,2) =GC suffix(s,0) =

s1u, s=ut, tu

(killer agent)1

||-1

, s = ATGCGGTAGC

s= TGCGGTAGCs = ATGCGGTAG ATGC GGTAG ? (ATGC ) GGTAG ATGC ( GGTAG )

stu=(st)u=s(tu); |s| -1, |t| -1, |u| -1

|st| = |s| + |t| ,st

1

s[ij]= i-1 s |s| -j

prefix(s, k) = s |s| -k

Suffic(s, k) = |s| -k s

homology- Orthologous paralogous

similarity

a1 in species I, a1 in species II)a1 and a2 in species I

Alignment s=GACGGATTAGt=GATCGGAATAGAlignment2: GA-CGGATTAGGATCGGAATAGAlignment1:GACGGATTAG GATCGGAATAG

()

4DNA{A, C, G, T}

IUPAC

IUPAC

GGGuanine AAAdenine TTThymine CCCytosineRG or APurine YT or CPyrimidine MA or CAmino KG or TKeto SG or CStrong interaction (3 H bonds) WA or TWeak interaction (2 H bonds) HA or C or TNot-GBG or T or Cnot-AVG or C or Anot-T(not-U) DG or A or Tnot-C NG or A or T or CAny

DNA

1

2

3

4

54

(global alignment)

s=ATTGCATATGt=ATTGATATC

s=ATTGCATATGt=ATTG ATATC

121

s, t2sim(s, t)=max{score i}

s=ATTGCATATG s=ATTGCATATG t=ATTG ATATC; t=ATTG ATATC8(-2)(-1)=5 4+ (-2) + (-1) 5 =-1

2.

st(local alignment)st

s=AATTGCATATGt=ATTGT

s(2,3,4,5)=t(1,2,3,4)

3.

st

s=AATTGCATATGt=ATTGTs=AATTGCATATG s=AATTGCATATGt= - ATTGT - - - - - t= A- TTG - - T - - -

2

2sim(s, t)max{score i}

s t; t=AGCTT; s=TTA TTA - - TTA AGTTA AGCTAAGCTT

1 2

(cost)

dist(s,t)=min{cost i}

ACCGACAATATGCATA ATAGGTATAACAGTCAACCGACAATATGCATA ACTGACAATATGGATA

RNA

1 2

1 1

108108

aHomo sapiensPongo pygmaeusb108 (a) (b)

DNA

DNA

DNA

(fragment assembly)

fragment

ATTGGGCA; CGATT; TGGGCAGA - - ATTGGGCA - -CGATT - - - - - - - - - - - TGGGCAGA

CGATTGGGCAGA

(shortest common superstring)

(reconstruction)

(multicontig)

DNA DNA

DNADNADNADNARNA

DNAPromoterTerminator sequenceSplice site

DNA

training setcontrol set

training setcontrol set

Sn Sp

TpTnFnFp

functional sitefunctional sequencemotifsignal

functional region

A common consensus : NTATN

1

215

GGAATTCCRG or AYT or CMA or CKG or TSG or C(3)WA or T(2)HA or C or TGBG or T or CAVG or C or AT(U)DG or A or TCNG or A or T or C

: (1) N(2) (3) 54(4) 2(5) N1

TTATGATATATACGCTTGTC TCCAC TTATGATATATACGCTTGTC TCCAC TNNNN tTATG tACGC tTGTC tCCAC tTATG tACGC tTGTC tCCAC TNNNC [1] [2] [3] [4] [2] [3] NNNNNTNNNN TNNNC tACGc tTGTc tCCAc [4] [2] tACGc tTGTc tCCAc [3] TNSNC [5] Consensus1 TNSNC TTATG ATATA [5] Consensus2 NTATN TNSNC

DNA

B

4n 4n

M(aj,j)aj,a {A,T,G,C}

s=a1a2an

S=ATTGCA Ws = 1+6+14-5+8+19=43 TTWs TSWs T'S

MA+ A- 1M 23-6 3SiSi A+ 4Si A-5 4WSi TMSiM16 5WSi TMSiM16 67 7M2

MM

DNA

ORF,open reading frame

()

21 64/3

DNAORFORFORF

() 641

DNA36:4:1

DNA

DNAORFORFORF

ORF

fabcabca1,b1,c1, a2,b2,c2,, an+1,bn+1a1b1c1n

n

i

3nPiPi

()

() :

sensitivitySnspecificitySp

() EST

() 53

() ,e1, i1, , in-1, en , ATG-1n-UAG

donor- gt acceptor- ag

gene A

i0, e1, i1, , en, in ij0jn el1ln i0in

DNA 13

2

3-i0, e1-en, in

sourcesink

() DNARNA

HPESE-mailWSwebCL/EXSC

RNA

RNA

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