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FASTA:

Mackey A.J., Haystead T.A., Pearson W.R. (2002)
Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences.
Molecular and Cellular Proteomics 1(2): 139-147.
abstract

Pearson W.R. and Lipman D.J. (1988)
Improved Tools for Biological Sequence Comparison.
PNAS 85:2444- 2448.
abstract

Pearson W.R. (1990)
Rapid and Sensitive Sequence Comparison with FASTP and FASTA.
Methods in Enzymology 183: 63-98.
abstract

Pearson W.R. and Lipman D.J. (1988)
Improved Tools for Biological Sequence Comparison.
Proceedings of the National Academy of Sciences 85: 2444-2448.
abstract

Pearson W.R. (1990)
Rapid and Sensitive Sequence Comparison with FASTP and FASTA.
Methods in Enzymology 183: 63-98.
abstract

BLAST:

Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and . Lipman D.J. (1997)
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic Acids Research 25(17): 3389-3402.
abstract

Shpaer E.G. , Robinson M., Yee D., Candlin J.D., Mines R., and Hunkapiller T. (1996)
Sensitivity and Selectivity in Protein Similarity Searches: Comparison of Smith-Waterman in Hardware.
Genomics 38: 179-191.
abstract

Altschul S.F. (1991)
Amino acid substitution matrices from an information theoretic perspective.
Journal of Molecular Biology 219: 555-565.
abstract

Altschul S.F. (1993)
A protein alignment scoring system sensitive at all evolutionary distances.
Journal of Molecular Evolution 36: 290-300.
abstract

Altschul S.F., Boguski M.S., Gish W. and Wootton J.C. (1994)
Issues in searching molecular sequence databases.
Nature Genetics 6: 119-129.
abstract

Pearson W.R. (1991)
Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.
Genomics 11(3): 635-650.
abstract

Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. (1990)
Basic local alignment search tool.
J. Mol. Biol. 215:403-10.
abstract

Claverie J.M. and States D.J. (1993)
Information enhancement methods for large scale sequence analysis.
Computers in Chemistry 17:191-201.


Gish W. and States D.J. (1993)
Identification of protein coding regions by database similarity search.
Nature Genetics 3: 266-272.
abstract

Henikoff S. and Henikoff J.G. (1992)
Amino acid substitution matrices from protein blocks.
Proceedings of the National Academy of Sciences USA 89: 10915-10919.
abstract

Karlin S. and Altschul S.F. (1990)
Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.
Proceedings of the National Academy of Sciences USA 87: 2264-2268.
abstract

Karlin, S. and Altschul S.F. (1993)
Applications and statistics for multiple high-scoring segments in molecular sequences.
Proceedings of the National Academy of Sciences USA 90: 5873-5877.
abstract

States D.J. and Gish W. (1994)
Combined use of sequence similarity and codon bias for coding region identification.
Journal of Computational Biology 1: 39-50.
abstract

States D.J., Gish W. and Altschul S.F. (1991)
Improved sensitivity of nucleic acid database similarity searches using application specific scoring matrices.
Methods: A companion to Methods in Enzymology 3: 66-70.


Wootton J.C. and Federhen S. (1993)
Statistics of local complexity in amino acid sequences and sequence databases.
Computers in Chemistry 17: 149-163.


SEQUENCE ALIGNMENT:

Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H.*, Valentin F.*, Wallace I.M., Wilm A., Lopez R.*, Thompson J.D., Gibson T.J. and Higgins D.G. (2007)
ClustalW and ClustalX version 2.
Bioinformatics 2007 23(21): 2947-2948.
abstract full-text PDF

Higgins D., Thompson J., Gibson T., Thompson J.D., Higgins D.G., Gibson T.J.(1994)
CLUSTAL W: improving the sensitivity of progressivemultiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice.
Nucleic Acids Research 22: 4673-4680.
abstract

Lopez R., Services Programme and Lloyd A. (1997)
ClustalW WWW Service at the European Bioinformatics Institute
http://www.ebi.ac.uk/Tools/clustalw2/
The ClustalW WWW server at the EBIembnet.news volume 4.2 1997
http://www.ebi.ac.uk/embnet.news/vol4_3/clustalw1.html

Lassmann T. and Sonnhammer E.L.L. (2006)
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.
Nucleic Acids Research 34: W596-W599.
abstract

Lassmann T. and Sonnhammer E.L.L. (2005)
Kalign - an accurate and fast multiple sequence alignment algorithm.
BMC Bioinformatics 6: 298.
abstract

Lassmann T. and Sonnhammer E.L.L. (2005)
Automatic assessment of alignment quality.
Nucleic Acids Research 33(22): 7120-7128.
abstract

Edgar R.C. (2004)
MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
BMC Bioinformatics 5: 113.
full-text HTML

Edgar R.C. (2004)
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Nucleic Acids Research 32(5): 1792-1797.

O'Sullivan O., Suhre K., Abergel C., Higgins D.G., Notredame C. (2004)
3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments.
Journal of Molecular Biology 340: 385-395.
full-text PDF

Notredame C., Higgins D., Heringa J. (2000)
T-Coffee: A novel method for multiple sequence alignments.
Journal of Molecular Biology 302: 205-217.
full-text PDF

Notredame C., Holme L. and Higgins D.G. (1998)
COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
Bioinformatics 14(5: 407-422.
full-text PDF

Notredame C., Higgins D.G., Heringa J. (2000)
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Journal of Molecular Biology 302(1): 205-217.


MATRICES:

Altschul S.F. (1991)
Amino acid substitutions matrices from an information theoretic perspective.
Journal of Molecular Biology 219: 555-665.
abstract

Altschul S.F., Boguski M.S., Gish W. and Wootton J.C. (1994)
Issues in searching molecular sequence databases.
Nature Genetics 6: 119-129.
abstract

Dayhoff M.O., Schwartz R.M., Orcutt B.C. (1978)
A model of evolutionary change in proteins.
In "Atlas of Protein Sequence and Structure" 5(3) M.O. Dayhoff (ed.), 345 - 352.


Gonnet G.H., Cohen M.A., Benner S.A. (1992).
Exhaustive matching of the entire protein sequence database.
Science 256(5062): 1443-1445.
abstract

Henikoff S. and Henikoff J. (1992)
Amino acid substitution matrices from protein blocks.
Proceedings of the National Academy of Sciences USA 89(biochemistry): 10915-10919.
abstract

OTHERS:

Walsh T.P, Webber C., Searle S., Sturrock S.S, and Barton G.J. (2008)
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser
Nucleic Acids Research,Vol. 36, Web Server issue W25–W29.
full-text PDF.

Barton G.J. (2002)
"ScanPS Version 2.3.9 User guide",
University of Dundee, UK.
full-text PDF.

Zdobnov E.M. and Apweiler R. (2001)
InterProScan - an integration platform for the signature-recognition methods in InterPro.
Bioinformatics 17(9): 847-848.
abstract

Attwood T.K., Croning M.D.R., Flower D.R., Lewis A.P., Mabey J.E., Scordis P., Selley J. and Wright W. (2000)
PRINTS-S: the database formerly known as PRINTS.
Nucleic Acids Research 28(1): 225-227.
abstract

Bernardi G. (2000)
Isochores and the evolutionary genomics of vertebrates.
Gene 241(1): 3-17.
abstract

Heger A., Holm L. (2000)
Rapid automatic detection and alignment of repeats in protein sequences.
Proteins 41(2): 224-237.
abstract

Rice P., Longden I., Bleasby A. (2000)
EMBOSS: the European Molecular Biology Open Software Suite.
Trends in Genetics 16(6): 276-277.
abstract

Harrison R.G. (2000)
Expression of soluble heterologous proteins via fusion with NusA protein.
in inNovations 11: 4-7.


Thompson J.D., Plewniak F., Thierry J.C. and Poch O. (2000)
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches.
Nucleic Acids Research 28(15): 2919-2926.
abstract

Pesole G., Bernardi G., Saccone C. (1999)
Isochore specificity of AUG initiator context of human genes.
FEBS Letters 464(1-2): 60-62.
abstract

Brown N P., Leroy C., Sander C. (1998)
MView: a web-compatible database search or multiple alignment viewer.
Bioinformatics 14(4): 380-381.
abstract

Altschul S.F., and Gish W. (1996)
Local alignment statistics. ed. R. Doolittle.
Methods in Enzymology 266: 460-480.
abstract

Borodovsky M. and McIninch J. (1993)
GeneMark: parallel gene recognition for both DNA strands.
Computers and Chemistry 17(19): 123-133.


Sturrock S. and Collins J. (1993)
MPsrch version 1.3.
Biocomputing Research (1993).
Unit University of Edinburgh,
UK.


Brendel V., Bucher P., Nourbakhsh I., Blaisdell B.E., Karlin S. (1992)
Methods and algorithms for statistical analysis of protein sequences.
Proceedings of the National Academy of Sciences USA 89: 2002-2006.
abstract

Larsen F., Gundersen G., Lopez R., Prydz H. (1992)
CpG islands as gene markers in the human genome.
Genomics 13(4): 1095-1107.
abstract

Gardiner-Garden M., Frommer M. (1987)
CpG islands in vertebrate genomes.
Journal of Molecular Biology 196(2): 261-282.
abstract

Kabsch W. and Sander C. (1983)
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
Biopolymers 22(12): 2577-2637.
abstract

Kruskal J.B. (1983)
An overview of squence comparison.
In D. Sankoff and J. B. Kruskal, (ed.), Time warps, string edits and macromolecules: the theory and practice of sequence comparison, pp. 1-44 Addison Wesley.

Sweet R.M., Eisenberg D. (1983)
Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure.
Journal of Molecular Biology 171(4): 479-488.
abstract

Kyte J., Doolittle R.F. (1982)
A simple method for displaying the hydropathic character of a protein.
Journal of Molecular Biology 157(1): 105-132.
abstract

Eisenberg D., Weiss R.M., Terwilliger T.C. (1982)
The helical hydrophobic moment: a measure of the amphiphilicity of a helix.
Nature 299(5881): 371-374.
abstract

Smith T.F., Waterman M.S. (1981)
Smith and Waterman
Advances in Applied Mathematics 2: 482-489.


Smith T.F., Waterman M.S. (1981)
Identification of common molecular subsequences.
Journal of Molecular Biology 147: 195-197.
abstract

Needleman S.B. and Wunsch C.D. (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.
abstract

Holm L., Park J. (2000)
DaliLite workbench for protein structure comparison.
Bioinformatics 16: 566-567.
abstract