This tutorial was prepared by Mauricio La Rota for the Cornell University course PL BR 607 tought in the fall 2000 by Dave Schneider.
The handouts of the Dave
Schneider's lectures are available here (together with animation automaton). The three homeworks associated with the
course are available as well ( H1+ sequence,
H2 + sequence and
final homework).
The purpose of this page is to introduce the PB607 student to a few concepts used by sequence comparison programs as well as to the mechanics of what is probably the most used pieces of software when it comes to comparing biological sequences: The set of BLAST and FASTA programs, and then to introduce the multiple sequence alignment program ClustalW/ClustalX. The tutorials are meant to be VERY simple, targeted to the student who has never looked at similarity between biological sequences.
Please complete all readings before the start time of the PB607 course (middle October 2000).
( Click on the image: next to a title to go to that page:)
1
Bioinformatics: A Practical Guide to the Analysis
of Genes and Proteins
Andreas D. Baxevanis. B.F. Francis Ouellette
June 1998, (volume 39 of Methods of biochemical Analysis).
ISBN 471191965
John Wiley & Sons, Inc. New York, NY 10158-0012. Call number: QD271 M59 v.39
From this book: these are optional but recommended:
Chapter 1,2, Appendix 2
And these are required readings:
Pages 98,101-120.
Pages 145-188
2
Biological Sequence Analysis: Probabilistic Models
of Proteins and Nucleic Acids
Richard Durbin (Edt), Eddy, R. Krogh, A. Mitchison, G.
May 1, 1998
ISBN 0521620414 or 0-521-62971-3 (paperback)
Cambridge University Press
From this book, this is optional but recommended: Introductory chapter.
3
Jefferys W.H and Berger J.O. 1992. Okham's razor and Bayesian Analysis.
American Scientist 80:64-72 (is also available on reserve in Mann Library)
For Your Information:
A list of important terms is available in the local
glossary. (a few concepts were added to those already explained in
NCBI's
glossary)
If you need to check more books that relate to bioinformatics and computational
biology in general, there is a list
here: (Local
Book Table) and a second
one here (http://www.iscb.org/books.html)