Automated assembly of protein blocks for database searching
    - Henikoff S, Henikoff JG

Amino acid substitution matrices from protein blocks
    - Henikoff S, Henikoff JG

Finding sequence motifs in groups of functionally related proteins
    - Smith HO, Annau TM, Chandrasegaran S

Model of evolutionary change in proteins
    - Dayhoff, Schwartz, Orcutt

Optimal alignments in linear space
    - Myers EW, Miller W

A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons
    - Waterman MS, Eggert M

A space-efficient algorithm for local similarities
    - Huang, Hardison, Miller

A time-efficient, linear-space local similarity algorithm
    - Huang, Miller

Overview of sequence comparison algorithms in molecular biology
    - Myers

Basic local alignment search tool
    - Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    - Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ

Improved tools for biological sequence comparison
    - Pearson WR, Lipman DJ

Rapid and sensitive sequence comparison with FASTP and FASTA
    - Pearson WR

PatternHunter: faster and more sensitive homology search
    - Ma B, Tromp J, Li M

Designing Seeds for Similarity Search in Genomic DNA
    - Buhler J, Keich U, Sun Y

Designing multiple simultaneous seeds for DNA similarity search
    - Sun Y, Buhler J

Optimizing multiple spaced seeds for homology search
    -  Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma