LecturesPart03

3 saibj contains similarity scores for elements ai

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Unformatted text preview: s the penalty for a gap of length z>0 S0,0 initialized to 0 initialized S0,z initialized to wz for 0<z<n for Sz,0 initialized to wz for 0<z<m for Formal description of full dynamic programming algorithm Si, j = max{Si- 1, j - 1 + s(aib j ), max (Si- x, j - w x ), x³ 1 max (Si, j - y - w y )} y³ 1 s(aibj) similarity, wz gap penalty gap S0,0 = 0, S0,z = wz, Sz,0 = wz Method: Layout: Mismatch penalty: Gap penalty: Translation: Needleman-Wunsh -> Standard Smaller (1) Smaller (1) Off • 20 • 40 • 60 • 80 • 100 1 ATGAGCACAAAAAAGAAACCATTAACACAAGAGCAGCTTGAGGACGCACGTCGCCTTAAAGCAATTTATGAAAAAAAGAAAAATGAACTTGGCTTATCCC 100 |||| ||| || || | | | | | ||| || | |||| | | || |||||||| || || | | | | || 1 ATGAATACACAATTGA=====T========G=G==G=T=GAG==CGTAT=TCGCGCTC==G=AA=====GAAAAAAACTCAA==GAT=TAGACA=AGCC= 66 • 20 • 40 • 60 • 120 • 140 • 160 • 180 • 101 AGGAATCTGTCGCAGACAAGATGGGGATGGGGCAGTCAGGCGT-TGGTGCTTTATTT-AATGGCA----TC--A-A-TGCATTAAATGCTTATAACGCCG 190 | ||| | | | ||||||| |||| ||| | | || ||| ||| ||||| | || | | || ||||| | ||| | | 67 =GC==TCT=T=G==GT=AAGATGG===TGGG==AGT==GTCTAATGTTGCAATATCGCAATGGGAGCGCTCGGAGACTGAGCCAAATGGGGAGAAC=CTG 150 • 80 • 100 • 120 • 140 • 200 • 220 • 240 • 260 • 280 191 CATTGC--TTGCAAAAATTCT-CAAAGTTAGCGTTGAAGAATTTAGCCCTTCAATCGCCAGAGAAATCTACGAGATGTATGAAGCGGTTAGTATGC-AGC 286 | || || | || ||| || | | | | || | ||| || | || | |||| | || | | | | || || | ||| || 151 T=TGGCACTTTCGAAGGCTCTTCAGTGCTCCCCT=GACTA=TTT=GC==TGAAA==G===GAGAT=T=TAAGCCA=G=ACAAA=CGTTGCCTATCATAGT 234 160 • 180 • 200 • 220 • • 300 • 320 • 340 • 360 • 380 287 CGTCACTTAGAAGTGAGTATGAGTACCCTGTTTTTTCTCATGTTCAG-GCAGGGATGTTCTCACCTGAGCT-TAGAACCTTTACCAAAGGTGATGCGG-A 383 | || | || ||| || | |||||| || | | || || |||||| | | |||| ||||||||| | || | | | ||| | 235 AGGCA=TGAGCCAAGAGGATCA=TACCCTCTTATCAGTTGGGTA=AGCGCAGGGCAATGG==ATGGAAGCTGTAGAACCTT=ATCACAAGCGC=GCGATA 327 240 • 260 • 280 300 • 320 • 400 • 420 • 440 • 460 • 384 GAGATG-GGTAAG-CACAACCAAAAAA-GC-CAGT-GATTCTGCATTCTGGCTTGAGGTTGAAGGTAATTCCATGACCGCACCAACAGGCTCCAAGCCAA 478 |||| || | | ||| || | | | ||| ||||| ||| |||||||| || ||||| | || ||...
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This note was uploaded on 01/13/2012 for the course BIO 101 taught by Professor Staff during the Fall '10 term at DePaul.

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