Bioinformatics and Functional Genomics

Table 3-4. Global pairwise alignment algorithms. Abbreviations: EMBOSS, The European Molecular Biology Open Software Suite (http://emboss.sourceforge.net/); ISREC, Swiss Institute for Experimental Cancer Research (http://www.isrec.isb-sib.ch/).

Resource	Description
ALIGN	At the GENESTREAM server, France
Gap	From the Genetics Computer Group (GCG)
Needle	From the Institut Pasteur; implements Needleman-Wunsch global alignment
Pairwise alignment (various)	From the University of Virginia (Bill Pearson)
Pairwise	Two Sequence Alignment Tool (global and local options)
Pairwise Sequence Alignment	From the Baylor College of Medicine; various tools
Stretcher	From the Institut Pasteur; global alignment
Vector NTI Suite 7	From Informax, Inc.

 

Table 3-5. Local pairwise alignment algorithms. Abbreviations: EMBOSS, The European Molecular Biology Open Software Suite (http://emboss.sourceforge.net/); ISREC, Swiss Institute for Experimental Cancer Research (http://www.isrec.isb-sib.ch/).

Resource	Description
BESTFIT	From the Genetics Computer Group (GCG)
BLAST2sequences	at NCBI
est2genome	From the Institut Pasteur; aligns expressed sequence tags to genomic DNA
LALIGN	find multiple matching subsegments in two sequences
Pairwise alignment (various)	From the University of Virginia (Bill Pearson)
Pairwise	Two Sequence Alignment Tool (global and local options)
Pairwise Sequence Alignment	From the Baylor College of Medicine; various tools
PRSS	From the University of Virginia (Bill Pearson)
SIM	Alignment Tool for protein sequences from ExPASy
SIM	SIM, gap at The Dept. of Computer Science, Mich. Tech
SSEARCH	At the Protein Information Resource
Vector NTI Suite 7	From Informax, Inc.

 

Table 3-6. Dot plot algorithms.

Resource	Description
Dotlet	Makes dot plots; from ISREC