Pairwise Sequence Alignments

Methods and tools for aligning pairs of sequences.

Found 29 links

Displaying 15 links

ChinookTool Content

http://www.bcgsc.bc.ca/chinook/

Chinook is a peer-to-peer (P2P) service for the discovery, use and assessment of bioinformatics programs. Chinook Online allows researchers to connect and run distributed bioinformatics programs using a web application.

CrossLinkTool Content

http://www-ab.informatik.uni-tuebingen.de/software/crosslink/webstart/welcome.ht...

Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.

DotletTool Content

http://www.isrec.isb-sib.ch/java/dotlet/Dotlet.html

Dot plot tool with very helpful learn by example interpretations of sample outputs.

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FFASTool Content

http://ffas.godziklab.org

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

LAGANTool Content

http://lagan.stanford.edu/lagan_web/index.shtml

The LAGAN alignment toolkit consists of components: CHAOS (a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome.), LAGAN (a highly parametrizable pairwise global alignment program), Multi-LAGAN , and Shuffle-LAGAN (both variations of LAGAN).

MATRASTool Content

http://strcomp.protein.osaka-u.ac.jp/matras/

MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures.

MGIPTool Content

http://mgip.biology.gatech.edu

The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize the specific sequence type and clonal complex of the Neisseria meningitidis strain.

MIGenAS ToolkitTool Content

http://www.migenas.org/

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

MPSRCHTool Content

http://www.ebi.ac.uk/MPsrch

Uses the Smith-Waterman algorithm; runs at BLAST-like speeds without losing sensitivity.

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OrthoSelectTool Content

http://orthoselect.gobics.de

OrthoSelect web server detects orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Annotations, data matrices for each gene, and the gene alignments may also be visualized.

Tags associated with subcategory 'Sequence Comparison/Pairwise Sequence Alignments'

sequence alignment algorithms genomics dna sequence analysis nucleic acid sequence homology amino acid sequence homology protein databases computational biology molecular evolution markov chains molecular models salmonella time factors sensitivity and specificity secondary protein structure protein structural homology proteins gene deletion nucleotidyltransferases viral dna variola virus vaccinia virus technology transfer thermoplasma viral genes viral genome nucleic acid regulatory sequences gene components escherichia coli viral proteins enterobacteriaceae protein folding systems integration mice humans human genome genome molecular sequence data pan troglodytes takifugu swine rats papio dogs chickens conserved sequence binding sites bacterial genome bacterial dna mycobacterium leprae mycobacterium tuberculosis cattle base sequence sequence analysis transcription factors data display statistical data interpretation zebrafish genes plant lectins complementary dna capripoxvirus membrane proteins alleles bacterial typing techniques rna sequence analysis rna nucleic acid conformation neisseria meningitidis reproducibility of results canada biological models benchmarking micrornas amino acid substitution chromosome mapping expressed sequence tags biomedical technology assessment base composition roc curve molecular biology animals microcomputers amino acid sequence untranslated rna computing methodologies nucleic acid databases mutation multimedia genetic databases multigene family nucleotides open reading frames reference standards protein sequence analysis programming languages phylogeny poxviridae fuzzy logic factual databases protein conformation