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