References
Altschul SF and
Gish W
(1996)
Local alignment statistics.
Methods in Enzymology
266: 460–480.
Altschul SF,
Gish W,
Miller W,
Myers EW and
Lipman DJ
(1990)
Basic local alignment search tool.
Journal of Molecular Biology
215: 403–410.
Dayhoff M,
Schwartz RM and
Orcutt BC
(1978)
A model of evolutionary change in proteins.
Atlas of Protein Sequence and Structure,
vol. 5 (supplement 3),
pp. 345–358.
Silver Springs, MD: National Biomedical Research Foundation.
Doolittle RF
(1986)
Of Urfs and Orfs: Primer on How to Analyze Derived Amino Acid Sequences.
Mill Valley, CA: University Science Books.
Feng DF and
Doolittle RF
(1987)
Progressive sequence alignment as a prerequisite to correct phylogenetic trees.
Journal of Molecular Evolution
25: 351–360.
Needleman SB and
Wunsch CD
(1970)
A general method applicable to the search for similarities in the amino acid sequence of two proteins.
Journal of Molecular Biology
48: 443–453.
Pearson WR
(1998)
Empirical statistical estimates for sequence similarity searches.
Journal of Molecular Biology
276: 71–84.
Pearson WR and
Lipman DJ
(1988)
Improved tools for biological sequence comparison.
Proceedings of the National Academy of Sciences of the United States of America
85: 2444–2448.
Sankoff D
(1975)
Minimal mutation trees of sequences.
SIAM Journal of Applied Mathematics
78: 35–42.
Smith TF and
Waterman MS
(1981)
Identification of common molecular subsequences.
Journal of Molecular Biology
215: 403–410.
States DJ and
Boguski MS
(1991)
Similarity and homology.
In: Gribskov M and
Devereux J (eds.)
Sequence Analysis Primer,
pp. 92–124.
NewYork, NY: Stockton Press.
Thompson JD,
Higgins DG and
Gibson TJ
(1994)
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position‐specific gap penalties and matrix choice.
Nucleic Acids Research
22: 4673–4680.
Further Reading
Altschul SF
(1991)
Amino acid substitution matrices from an information theoretic perspective.
Journal of Molecular Biology
219: 555–565.
Apostolico A and
Giancarlo R
(1998)
Sequence alignment in molecular biology.
Journal of Computational Biology
5: 173–196.
Benner SA,
Cohen MA and
Gonnet GH
(1993)
Empirical and structural models for insertions and deletions in the divergent evolution of proteins.
Journal of Molecular Biology
229: 1065–1082.
Durbin R,
Eddy S,
Krogh A and
Mitchison G
(1999)
Pairwise alignment.
Durbin R (ed.)
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids,
pp. 12–45.
Cambridge, UK: Cambridge University Press.
Gotoh O
(1999)
Multiple sequence alignment: algorithms and applications.
Advanced Biophysics
36: 159–206.
Henikoff S and
Henikoff JG
(1993)
Performance evaluation of amino acid substitution matrices.
Proteins
17: 49–61.
Henikoff S
(1994)
Comparative sequence analysis: finding genes.
In: Smith DW (ed.)
Biocomputing, Informatics and Genome Projects,
pp. 87–117.
New York, NY: Academic Press.
Smith TF
(1999)
The art of matchmaking: sequence alignment methods and their structural implications.
Structure with Folding and Design
7: R7–R12.
Vogt G,
Etzold T and
Argos P
(1995)
An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited.
Journal of Molecular Biology
249: 816–831.
Waterman MS
(1995)
Dynamic programming alignment of two sequences.
In: Michael SW (ed.)
Introduction to Computational Biology: Maps, Sequences and Genomes,
pp. 183–232.
London, UK: Chapman & Hall/CRC Press.
Yona G and
Brenner SE
(2000)
Comparison of protein sequences and practical database searching.
In: Higgins DG and
Taylor WR (eds.)
Bioinformatics: Sequence, Structure and Databanks. A Practical Approach,
pp. 167–190.
Oxford, UK: Oxford University Press.
Web Links
Blocks database http://www.blocks.fhcrc.org/