Spring 2007
MCB 396 section 42
(2 credit)

Programming Exercises in Perl for Biologists

Meeting Time:
Thursday, 1.45-3.50PM

Meeting Place: BP201 (Biology Physics Bldg, second floor)


Instructor: J. Peter Gogarten,
Office: BSP 404, phone: 486-4061,
email: gogarten@uconn.edu

 

 

 

Listing of example programs (to cannibalize) last updated 3/23

Class 12: discussion student projects, bioperl, coalescence

Class 11: Quartets, spectral decomposition and coalescence

Class 10: From multiple alignment to phylogenetic tree and model -- Phylip, Puzzle, Phyml, MrBayes

Class 9: PSIblast from the command line, phylogenetics overview

Class 8: Formatdb, BLAST, pepstat

Class 7: BLASTALL, gnuplot

Classs 6: Sequence alignment and Intro to Regular Expressions

Class 5: Use of Hashes to count oligonucleotide frequencies. use of system to run unix programs

Class 4: Input from a file, hashes, first pattern matches

Class 3: Loops, Arrays, Lists, first example to hand a filename to the program and to read from the file.

Class 2: Numerical operators, binary assignment operators, comparison and logic. Example of control structures.

Class 1: UNIX / Mac OSX, accounts, vi, ssh, textwrangler, variable types, number manipulation, interpolation, assignments, evaluations


The amount of molecular and biological data available in various data banks has exploded in recent years thanks to many completed and ongoing genome sequencing projects and due to many genome and proteome scale analyses. The number of programs used to analyze these data has increased with nearly equal speed.

The ability to handle large amounts of data has become a daily routine for many biologists; however, web based servers often are slow and cumbersome to use for repetitive tasks. Simple scripting tools provide an easy way for biologists to adapt programs to the tasks they want to perform. Perl is a computer language popular among biologists and bioinformaticians because it is easy to learn and allows to parse the complicated output of other programs. This course will not turn biologists into computer scientists, rather it will enable biologists to use computational tools more effectively.

After introducing the basics of PERL, the course will focus on programs that allow simple genome analyses, databank searches (BLAST, local databanks), multiple sequence alignments (muscle, clustal, ...) and phylogenetic reconstruction (PHYLIP, PHYML, PAML). Each student will complete an independent project.

No textbook required - handouts and online reading materials will be provided.



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