CS 485-585: Bioinformatics and Computational Biology
Instructor: Jugal Kalita
- The Human Mitochondrial
DNA Sequence ; Wikipedia article on Mitochondrial Genome
; Database of Complete Mitochondrial Genomes: Accompanying paper
- DNA and RNA
- Alphabets: DNA, RNA and Amino Acid names and letters used in sequences
- Why are proteins important: why do we talk about proteins so much in bioinformatics?
- The Central Dogma of Molecular Biology: Information flows from DNA to RNA to protein, never from protein to DNA; a layman's description
- The Genetic Code: a sequence of three characters (called a codon) on the DNA (or corresponding mRNA) codes what amino acid will be created by the codon.
- Protein transcription and translation: a short animation ; another animation
- Protein Structure: An article from Wikipedia; A very short video
- A description of the Human Genome from Genome 2 by T.A. Brown
- Single Nucleotide Polymorphism Database : For example, if you want to find all the SNPs associated with human beings on Chromosome 1, click on Limits, choose Homo sapiens as Orgranism, choose Chromosome 1, and under Annotation choose OMIM. Keep the search term empty.
- A n introduction to Genome Rearrangement
- An introduction to Phylogenetics
- The Web Page for Searching for a Protein
Sequence using Swiss-Prot
- Results for An Example Search in Swiss-Prot
and TrEMBL for all proteins that have the string "Horse" in their
- The Details of the Protein A1A1_Horse (P18907)
in the Swiss-Prot Database
- The Web
Page for Searching for a Protein Sequence using PIR: Protein Information Resource
at Georgetown University
- Results of An Example Search in PIR Databae for all
proteins that have the string "Horse" in the name, 2/8/2004
- The Details of the Protein CCHO of horse in the
- The Protein Data Bank: See details
of protein sequence and structure (For example, type in "E. coli"
and do a "Full text search", lots of results come back, click on
one protein (say, 196L), and then click on "View Structure" or "Sequence
Search for genes. E.g., you can enter the term "Cancer" in the box
on the top of the page and Search the "OMIM" database for genes
that have been identified to be responsible for cancers of various kinds
Genome Assembly: Shotgun sequencing, Genome Sequence Assembly: Algorithms and Issues (Pop et al. 2002), de Bruin graphs, Eulerian Path and Circuit, An Eulerian Path Approach to DNA Fragment Assembly (Pevzner et al. 2001)
Two recent articles from the New York Times: Technology Lowers Cost of Deconding a Genome by Nicholas Wade (August 11, 2009) and I.B.M. Joins Pursuit of $1,000 Personal Genome by John Markoff (October 6, 2009)
- Paper by D. Pushkarev, N. Neff and S. Quake. This is the paper referrred to by the August 11, 2009 New York times article listed above: Single-molecule sequencing an individual human genome in Nature Biotechnology, Volume 27, No. 9, pp. 847-850
- Dot plots: Chapter 5 of Lesk's text pp. 242-254
- Alignment of two sequences: The Longest Common Subsquence Problem, Dynamic Algorithm, Read an algorithms textbook such as Cormen et al.
Chapter 2 of Durbin et al.: Pairwise Alignment