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BIPG 6100/8100 - Introduction to Bioinformatic Computation
Syllabus – Spring 2013 *
All classes are held in the BPG computer classroom, HEB 127, beginning Monday, January 14, 2013
The purpose of this course is to introduce students to use of computers to solve biological problems. The following will be included:
1) Use of the LINUX operating system
2) Use of PERL programming languagefor bioinformatic analysis
3) Use of bioinformatic programs on a desktop computer (local, BLAST, REPEATMASKER, CLUSTALW)
4) Database management (generation of Exon-Intron Database
Alexei Fedorov, Ph.D.
Office: Room 12 RHC
Head of Bioinformatics Lab
Department of Medicine
WEEK 1 (3h)
Introduction to computer science for biological tasks. What biologists should know
Introduction to the LINUX platform.
Working in a LINUX environment, part 1: basic UNIX commands. (ls, cat, pwd, cd, mkdir, rm, mv, cp, more, less, chmod etc…).
WEEK 2 (3h)
Working in a LINUX environment, part 2: a) working with large text databases;
b) simple programming in UNIX (pipelines; grep, sort, vi).
Introduction to PERL.
Practicing in PERL 1: variables and arrays; operators for strings and arrays; opening files and printing into files.
WEEK 3 (3h)
Introduction to PERL continued.
Practicing in PERL : regular expressions.
Practicing in PERL: more about regular expressions.
Substitutions, transliteration, match variables
WEEK 4 (3h)
Control structures (if, else, elsif, unless); Loops (for, foreach, while); Operators:
last, next; Blocks.
WEEK 5 (3h)
Associative arrays; multidimensional arrays, arrays of hashes.
WEEK 6 (3h)
Local BLAST: installation from NCBI; choosing parameters for blast; preparation of
local databases for BLAST; running the program.
Invoking BLAST inside Perl scripts (system calls).
Analysis of BLAST output using Perl scripts.
WEEK 7 (3h)
Other useful local programs and databases: RepeatMasker program, Repeat Database;
ClustalW for multiple alignments.
WEEK 8 (3h)
Creation of Exon-Intron Database from GenBank Current release
Downloading GenBank database
WEEK 9 (3h)
2-D genomic gel electrophoresis in silico.
WEEK 10 (3h)
Algorithm optimization for sequence analysis.
Comparisons of vast genomic sequences.
Designing a new program.
WEEK 11 (3h)
Random number generator; Monte Carlo simulations.
WEEK 12 (3h)
BioPerl; subroutines, packages, modules, and objects.
WEEK 13 (3h)
Other computer languages (includes 2h lecture (invited speakers) and 2h lab )
WEEK 14 (3h)
Database management, SQL language (includes 2h lecture (invited speakers) and 2h lab)
WEEK 15 (3h)
Practicing with object-oriented programming.
WEEK 16 (3h)
* Exam weeks are not included