- Altschul, SF., Boguski, MS., Gish, W., & Wootton, JC. Issues in searching molecular sequence databases. Nature Genetics 6:119-129. 1994.
- An extensive how-to guide, with emphasis on BLAST.
- Doolittle, RF. Similar amino acid sequences: chance or common ancestry Science 214:149-59 (1981)
- An excellent review from a pioneer in sequence searching. While many newer tools now exist, the common-sense guidlines in this classic article are must reading.
- Henikoff, S. Comparative sequence analysis: Finding genes. In Biocomputing, Informatics and Genome Projects. D.W. Smith ed. 1994. 87-117,
- A good introduction into the basics of sequence analysis, including discussions of the actual mechanics of alignment, the characteristics of various alignment algorithms, and block-type searching.
- Gribskov, M., & Devereaux, J., ed. Sequence analysis primer. Stockton Press. 1991.
- Oriented towards the GCG package.
- Doolittle, RF., ed. Molecular evolution: computer analysis of protein and nucleic acid sequences. Methods in Enzymology, vol 183. Academic Press. 1989.
- Like many of the Methods in Enzymology series, a mixture of how-to reviews and (then) cutting-edge research projects.
- Doolittle, RF. Of urfs and orfs: a primer on how to analyze derived amino acid sequences. University Science Books (Mill Valley CA) 1986.
- Heijne, G.von. Sequence analysis in molecular biology: treasure trove or trivial pursuit? Academic Press. 1987.
- From Amos Bairoch. Abstracts available for many entries.
- Citations only.
This document is intended to serve as a guide to using certain bioinformatics
programs. Comments about these sources represent the personal opinion of the author.
It cannot be guaranteed to be free of errors or completely up-to-date (particularly at this time -- it is an unfinished work-in-progress).
If you know of errors or other shortcomings of this document, please mail them
to Keith Robison