{[ promptMessage ]}

Bookmark it

{[ promptMessage ]}

LecturesPart03

# 3 saibj contains similarity scores for elements ai

This preview shows page 1. Sign up to view the full content.

This is the end of the preview. Sign up to access the rest of the document.

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 |||| || | | ||| || | | | ||| ||||| ||| |||||||| || ||||| | || ||...
View Full Document

{[ snackBarMessage ]}

### What students are saying

• As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

Kiran Temple University Fox School of Business ‘17, Course Hero Intern

• I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

Dana University of Pennsylvania ‘17, Course Hero Intern

• The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

Jill Tulane University ‘16, Course Hero Intern