Slide 1 Lecture 1 BNFO 601 Usman Roshan Slide 2 Course overview Perl progamming language (and some Unix basics) –Unix basics –Intro Perl exercises –Dynamic programming…

Slide 1 Lecture 1 BNFO 135 Usman Roshan Slide 2 Course overview Perl progamming language (and some Unix basics) –Unix basics –Intro Perl exercises –Programs for comparing…

Slide 1 The (Supertree) of Life: Procedures, Problems, and Prospects Presented by Usman Roshan Slide 2 Supertree Methods Input: Set of trees Output: Tree leaf-labeled by…

Slide 1 BNFO 602 Lecture 2 Usman Roshan Slide 2 Sequence Alignment Widely used in bioinformatics Proteins and genes are of different lengths due to error in sequencing and…

Slide 1 BNFO 602 Lecture 1 Usman Roshan Slide 2 Bio background DNA Transcription and translation Proteins: folding and structure SNPs SNP genotyping, sequencing Slide 3 Representing…

Slide 1 http://creativecommons.org/licenses/by-sa/2.0/ Slide 2 CIS786, Lecture 3 Usman Roshan Slide 3 Maximum Parsimony Character based method NP-hard (reduction to the Steiner…

Slide 1 Lecture 4 BNFO 235 Usman Roshan Slide 2 IUPAC Nucleic Acid symbols Slide 3 IUPAC Amino Acid symbols Slide 4 Genetic code Slide 5 Splitting and joining strings split:…

Slide 1 BNFO 602 Lecture 2 Usman Roshan Slide 2 Bioinformatics problems Sequence alignment: oldest and still actively studied Genome-wide association studies: new problem,…

Slide 1 Lecture 1 BNFO 136 Usman Roshan Slide 2 Course overview Pre-req: BNFO 135 or approval of instructor Python progamming language and Perl for continuing students –Some…

Slide 1 http://creativecommons.org/licenses/by-sa/2.0/ Slide 2 CIS786, Lecture 4 Usman Roshan Slide 3 Iterated local search: escape local optima by perturbation Local optimum…