Servers & Software for Generating Alignments
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[GeneStream] A global alignment of two nucleic acid sequences with no short-cuts.
[Stanford Univ.] A multiple sequence alignment tool.
AMAS: Analyze Multiple Alignments of Protein Sequences
[EBI] Allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree.
[EBI] A suite of programs for multiple protein sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures, and also implements flexible pattern matching and database scanning options.
BCM Search Launcher: Multiple Sequence Alignments
[Baylor College of Medicine] A single page offering services for several multiple alignment methods.
Bioinformatics & Pattern Discovery
[IBM] Information and bioinformatics related servers developed at IBM. Services include sequence pattern analysis, gene expression analysis, and multiple sequence alignment. Servers may be used online, or the code may be downloaded.
[Fred Hutchinson Cancer Research Center] “Block Maker finds conserved blocks in a group of two or more unaligned protein sequences, which are assumed to be related, using two different algorithms. At least
two protein sequences must be provided to make blocks.”
[Baylor College of Medicine] A multiple sequence alignment program for DNA and protein sequence parameters.
[GenomeNet] A general purpose multiple alignment program for DNA or proteins.
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[SGI] This is a multiple sequence alignment program for biological sequences.
[EBI] ClustalW is a popular and improved multiple alignment program for DNA or proteins.
[GSF] DIALIGN is a novel program for multiple alignment. It constructs pairwise
and multiple alignments by comparing whole segments of the sequences. No gap penalty is used. This approach is
especially efficient where sequences are not globally related but share only local similarities, as is the case with
genomic DNA and with many protein families.
Fast Local Alignment for Gigabases
The Fast Local Alignment for Gigabases site offers Cluster FLAG, a sequence database searching tool based on local
alignment of nucleotide sequences, and Pairwise FLAG to perform local alignment between two DNA
sequences, especially powerful for genome-genome
[Stanford University] (Luciano Brocchieri) A program for the multiple alignment of protein sequences.
LAMA: Local Alignment of Multiple Alignments
[Fred Hutchinson Cancer Research Center] This program compares multiple protein sequence alignments with each other. The program can search databases of such multiple alignments. The search is for sequence similarities between conserved regions of protein families.
[Sealy Center for Structural Biology] MASIA (Multiple Aligned Sequences Investigation and Analysis) is a program with GUI to search for
consistent patterns in multiple aligned sequences. Predictions of secondary structures and inside/outside properties of
residues at each position in an aligned sequences are based on generalized rules for globular proteins, which are
derived from observations of known 3D-structures of proteins.
[University of Namur] “The Match-Box software proposes protein sequence alignment tools based on strict statistical criteria. The Match-Box program is particularly suitable for finding and aligning conserved structural motives, in particular in protein core.”
[NPSA] “Multiple Protein Sequence Analysis is a stand-alone software package for protein sequence analysis with a high integration level and Web
client/server capabilities. It provides many methods and tools, which are integrated into an interactive graphical user
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MSA: Multiple Sequence Alignment
[Washington Univ.] Reads a file containing several protein sequences and attempts to produce a multiple alignment of these sequences, which it will write to standard output. MSA uses the algorithm of Altshcul et al., Gupta et al. or ClustalW.
[INRA] “Multalin creates a multiple sequence alignment from a group of related sequences using progressive pairwise alignments.”
[National Institute for Medical Research] Converts the results of BLAST, FASTA, and other sequence database searches to a coloured multiple alignment of hits stacked against the query.
Network Protein Sequence @nalysis
[Institute of Biology and Chemistry of Proteins] [email protected] is an interactive Web server dedicated to protein sequence analysis. Analyses offered include sequence similarity, site detection, multiple alignment, secondary structure prediction, and primary structure analysis. Analyses can be combined in a pipeline. The ANTHEPROT windows program is also available here.
[Pathogenomics Project, Univ. British Columbia] Do molecular phylogenetics analysis of a protein sequence. Enter the sequence at the site. PhyloBLAST uses BLASTP to find related amino acid sequences in the Swiss-Prot database. Select those sequences desired, for a full phylogenetic analysis, satrting with a ClustalW multiple sequence alignment. A choice of Phylip programs, including parsimony, UPGMA, neighbor joining and distance matrix methods, produces a phylogenetic tree.
PROBE ftp Site
[NCBI] PROBE is a tool for extraction of multiple alignments from a sequence database.
[Centre National de la Recherche Scientifique] Sequence Alignment by Genetic Algorithm. SAGA is optimally designed for the alignment of less than 20 sequences and less than 400 residues.
Secondary Structure Alignment Server
[Rutgers] The secondary structure alignment server is an
interactive tool that allows sequence alignments
to be performed based on iterative combinations
of amino acid and secondary structure sequence