423f11-lec2b

423f11-lec2b - String Comparison CMSC 423 Why compare DNA...

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Unformatted text preview: String Comparison CMSC 423 Why compare DNA or protein sequences? Partial CTCF protein sequence in 8 organisms: H. sapiens-EDSSDS-ENAEPDLDDNE D EEEPAVEIEPEPE----------PQPVTPA P. troglodytes-EDSSDS-ENAEPDLDDNE D EEEPAVEIEPEPE----------PQPVTPA C. lupus-EDSSDS-ENAEPDLDDNE D EEEPAVEIEPEPE----------PQPVTPA B. taurus-EDSSDS-ENAEPDLDDNE D EEEPAVEIEPEPE----------PQPVTPA M. musculus-EDSSDSEENAEPDLDDNE E EEEPAVEIEPEPE--PQPQPPPP PQPVAPA R. norvegicus-EDSSDS-ENAEPDLDDNE E EEEPAVEIEPEPE PQPQPQPQPQ PQPVAPA G. gallus-EDSSDSEENAEPDLDDNE D EEE T AVEIEAEPE---------- VSAE APA D. rerio DD D DD DS D E HG EPDLDD IDE E D E DDL-LDEDQMGLLDQAPPSVPIP- APA Identify important sequences by Fnding conserved regions. ind genes similar to known genes. Understand evolutionary relationships and distances (D. rerio aka zebraFsh is farther from humans than G. gallus aka chicken). Interface to databases of genetic sequences. As a step in genome assembly, and other sequence analysis tasks. Provide hints about protein structure and function (next slide). Sequence can reveal structure 1dtk XAKY C KL P LRI GPCK RK I PSFY Y KW KA KQ C LP F D Y S GC GGNA N R FK TI E E C R RTC V G- 5pti RPDF C LE P PYT GPCK AR I IRYF Y NA KA GL C QT F V Y G GC RAKR N N FK SA E D C M RTC G G A (a) 1dtk (b) 1dtk Sequence can reveal structure 1dtk XAKY C KL P LRI GPCK RK I PSFY Y KW KA KQ C LP F D Y S GC GGNA N R FK TI E E C R RTC V G- 5pti RPDF C LE P PYT GPCK AR I IRYF Y NA KA GL C QT F V Y G GC RAKR N N FK SA E D C M RTC G G A (a) 1dtk (b) 1dtk 5pti The Simplest String Comparison Problem Given : Two strings a = a 1 a 2 a 3 a 4 ... a m b = b 1 b 2 b 3 b 4 ... b n where a i , b i are letters from some alphabet like {A,C,G,T}....
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This note was uploaded on 01/13/2012 for the course CMSC 423 taught by Professor Staff during the Fall '07 term at Maryland.

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423f11-lec2b - String Comparison CMSC 423 Why compare DNA...

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