Further Reading

• Reviews

  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.

• Books

  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.

  Bibliographies

  SeqAnalRef

  From Amos Bairoch. Abstracts available for many entries.

  GenTools

  Citations only.