Lecture.pptVIP

Lecture 1 BNFO 136 Usman Roshan Course overview Pre-req: BNFO 135 or approval of instructor Python progamming language and Perl for continuing students Some unix basics Input/output, lists, dictionaries, loops, if-else, counting Sequence analysis Comparison of protein and DNA sequences Scoring a sequence alignment Picking the best alignment from a set Computing a sequence alignment Finding the most similar sequence to a query Overview (contd) Grade: 15% programming assignments, two 25% mid-terms and 35% final exam Recommended Texts: Introduction to Bioinformatics by Arthur M. Lesk Beginning Perl for Bioinformatics by James Tisdall Python Scripting for Computational Science by Hans Petter Langtangen Nothing in biology makes sense, except in the light of evolution Representing DNA in a format manipulatable by computers DNA is a double-helix molecule made up of four nucleotides: Adenosine (A) Cytosine (C) Thymine (T) Guanine (G) Since A (adenosine) always pairs with T (thymine) and C (cytosine) always pairs with G (guanine) knowing only one side of the ladder is enough We represent DNA as a sequence of letters where each letter could be A,C,G, or T. For example, for the helix shown here we would represent this as CAGT. Transcription and translation Amino acids Protein structure Getting started FASTA format: human ACAGTAT mouse ACGTA cat AGGTGAAA Python basics Basic types: Scalar: number or a string, Lists: collection of objects Dictionaries: collection of (key,value) pairs Reading sequences from a file into a data structure Basic if-else conditionals and for loops Some simple programs How many sequences in a FASTA file? What is the length and name of the longest and shortest sequence? What is the average sequence length? Verify that input contains DNA sequences. Compute the reverse complement of a DNA sequence Two dimensional lists Represented as list of lists For example the matrix 23 4 1 12 5 12 6 20 would be stored as [ [23, 4, 1], [12, 5, 12], [1, 6, 20] ]