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Table 3.1. Web sites for alignment of sequence pairs
Name of site		Web address		References
Bayes block alignera	http://www.wadsworth.org/resnres/bioinfo	Zhu et al. (1998)
Likelihood-weighted sequence alignmentb	http://stateslab.bioinformatics.med.umich.edu/service	see Web site
PipMaker (percent identity plot), a graphical tool for assessing long alignments	http://www.bx.psu.edu/miller_lab/	Schwartz et al. (2000)
BCM Search Launcherc	http://searchlauncher.bcm.tmc.edu/	see Web site
SIM—Local similarity program for finding alternative alignments	http://us.expasy.org/	Huang et al. (1990); Huang and Miller (1991); Pearson and Miller (1992)
Global alignment programs (GAP, NAP)	http://genome.cs.mtu.edu/align/align.html	Huang (1994)
FASTA program suited	http://fasta.bioch.virginia.edu/	Pearson and Miller (1992); Pearson (1996)
Pairwise BLASTe	http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html	Altschul et al. (1990)
AceViewf shows alignment of mRNAs and ESTs to the genome sequence	http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly	see Web site
BLATf Fast alignment for finding genes in genome	http://genome.ucsc.edu	Kent (2002)
GeneSeqerf predicts genes and aligns mRNA and genome sequences	http://www.bioinformatics.iastate.edu/bioinformatics2go/	Usuka et al. (2000)
SIM4f	http://globin.cse.psu.edu	Floria et al. (1998)
a See Chapter 4 for description and examples.     b A description of the probabilistic method of aligning two sequences is described in Durbin et al. (1998) and Chapter 4. A related topic, hidden Markov models for multiple sequence alignments, is discussed in Chapter 5.     c This server provides access to a number of Web sites offering pair-wise alignments between nucleic acid sequences, between protein sequences, or between a nucleic acid and a protein sequence.     d The FASTA algorithm normally used for sequence database searches (see Chapter 6) provides an alternative method to dynamic programming for producing an alignment between sequences. Briefly, all short patterns of a certain length are located in both sequences. If multiple patterns are found in the same order in both sequences, these provide the starting point for an alignment by the dynamic programming algorithm. Older versions of FASTA performed a global alignment, but more recent versions perform a local alignment with statistical evaluations of the scores. The program PLFASTA in the FASTA program suite provides a plot of the best-matching regions, much like a dot matrix analysis, and thus gives an indication of alternative alignments. The FASTA suite is also available from Genestream at http://vega.igh.cnrs.fr/. Programs include ALIGN (global, Needleman–Wunsch alignment), LALIGN (local, Smith–Waterman alignment), LALIGNO (Smith–Waterman alignment, no end gap penalty), FASTA (local alignment, FASTA method), and PRSS (local alignment with scrambled copies of second sequence to do statistical analysis). Versions of these programs that run with a command-line interface on MS-DOS and Macintosh microcomputers are available by anonymous FTP from ftp.virginia.edu/pub/fasta.     e The BLAST algorithm normally used for database similarity searches (Chapter 6) can also be used to align two sequences.     f Program useful for aligning expressed gene sequences (ESTs or mRNA) to genomic DNA.