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Overview

Computers and computer programs have become essential tools in modern molecular biology. As the amount of DNA and protein sequence data continues to grow, the use and understanding of these computational tools is becoming increasingly important. Deriving biological understanding from sequence data requires sophisticated computer analyses while demanding from molecular biologists the ability to interpret intelligently the results from these analyses. Not only can these programs provide the biologist with information about his or her sequence of interest, but a solid understanding of these tools can also be used to make predictions of biological phenomena that can be tested in the lab. This course will explore computational molecular biology through both lectures and hands-on computer experimentation through homework assignments.

This course will discuss approaches to analyzing protein and DNA sequences and will foster an understanding of how to extract biologically relevant information from the numerous databases containing all this information. Topics will include basic computer architecture and operating systems, database design and searching, sequence comparisons, pattern discovery, genome comparisons, gene discovery, determining evolutionary relationships, RNA and protein structure predictions, data mining, and DNA microarray analysis.

Instructions for submitting homework.

Prof. Gross is also doing a term project this term. This is a link to results he found so far. This file will be updated after each time he talks about his unknown during class. Last updated March 5, 2009.

Other Course Information

GenBank
SwissProt
EMBL
DDBJ
Blocks Database
Prosite Motif Database
BLOCKS Motif Database
BLIMPs (improved BLOCKs searching)
Clusters of Orthologous Groups (COGs)
FASTA searching
BLAST searching

arabadopsis
chimpanzee
drosophila
neurospora crassa
yeast
genome browser gateway
VISTA - genomic comparisons

Brookhaven Protein (PDB)
NCBI Structures
RNA
Structural Classification of Proteins (SCOP)
CHIME macromolecule database

DNA Array
biology newsgroups

Stanford Microarray Database
Europen Bioinformatics Institute
NCBI

Tools Used in This Course

A number of computer programs will be made available to you for use in this course. You should take advantage of these to complete your homework and term project. If you find other web sites that are useful please let me know so that I can add them to our list. Here are the programs that are for your use: