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Sequence Alignment Tools

• ALIGN Query: At the GENESTREAM network server IGH Montpellier FRANCE
• LALIGN - find multiple matching subsegments in two sequences
• SWBIC GraphAlign
• Lalign/Plalign: find internal duplications (By William R. Pearson and the University of Virginia)
• NdPASA: designed to optimize sequence alignment between distantly related proteins.(Reference: Li, W et al. 2005. Bioinformatics 21: 3803-3805)
• SIM - Alignment Tool for protein sequences: at ExPASy
• Secondary Structure Element Alignment (SSEA): alignments of protein secondary structures.(Reference: P. Fontana et al. (2005) Bioinformatics 21: 393-395)
• SUPERMATCHER
• MATCHER
• StretcherN: at EMBL-EBI
• NeedleN: at EMBL-EBI
• On-line help for CLUSTAL W
• ClustalW: multiple sequence alignment program for DNA or proteins
• DbClustal (Thompson et al. 2000. Nucleic Acid Research 28: 2919-2926; IGBMC, France)
• Gene Context Tool (Ciria R, Abreu-Goodger C, Morett E and Merino E (2004) GeConT: gene context analysis. Bioinformatics 20 (14): 2307-8.)
• Consensus: calculate the consensus for the CLUSTAL or MSF multiple alignment
• Multalin (Reference: F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890)
• DIALIGN: developed by Burkhard Morgenstern et al (at Bielefeld University Bioinformatics Server)
• T-COFFEE: This program is more accurate than ClustalW for sequences with less than 30% identity, but it is slower

RNA Alignment

• FOLDALIGN: folds and aligns RNA structures. (Reference: J. H. Havgaard et al. 2005. Bioinformatics 21: 1815 - 1824)
• MARNA: A Server for Multiple Alignment of RNAs (Reference: Sven Siebert and Rolf Backofen, "MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons", Bioinformatics 2005, Volume 21, Issue 16, 3352-3359 )

Alignment of long sequences or small genomes

• Pairwise FLAG (Fast Local Alignment for Gigabases)
• Advanced PipMaker (Schwartz et al., Genome Research 10:577-586, April 2000)
• JDotter: for generating dotplots of large DNA or protein sequences (Requires Java Runtime Environment)
• Softberry-Scan2 (Comparison of nucleotide sequences)
• Softberry-Scan2a (Comparison of protein sequences)
• YASS (Reference: L.Noe & G. Kucherov. 2005. Nucl. Acids Res. 33: W540-W543)
• zPicture: a dynamic alignment and visualization tool based on blastz alignment program (Comparative Genomics Center Lawrence Livermore National Laboratory 7000 East Ave., Livermore, CA 94550)
• VISTA: VISualization Tools for Alignments
• GeneOrder3.0: COMPARE GENE ORDER BETWEEN TWO SMALL BACTERIAL GENOMES
• COREGENES: Determines the core set of genes in a group of small genomes.

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