Pairwise Sequence Alignments

Methods and tools for aligning pairs of sequences.

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ALIGNTool Content

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Pairwise alignment is a tool designed for performing sequence alignments in a wide variety of combinations. It implements sequence to sequence, sequence to profile and profile to profile alignments with optional support of secondary structure. Different alignment options are freely selectable and include alignment types (local, global, free-shift) and number of sub-optimal results to report.

ChinookTool Content

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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.

CNVerTool Content

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CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage.

links directory index: 23
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Detecting copy number variation with mated short reads201023

CrossLinkTool Content

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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.

DIALIGNTool Content

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DIALIGN is a web server for pairwise and multiple DNA, RNA or protein sequence alignment using various sources of external information.

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DotletTool Content

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

This content is being maintained by myhits.

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DSPTool Content

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DSP is a shape string predictor for protein sequences. DSP provides both predicted shape string and sequence-shape string profile for each query sequence allowing for comparison of protein structure or evolution in shape string space.

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EBI ToolsTool Content

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EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies. Example tools include those to compute sequence similarity searches, pairwise/multiple sequence alignment and protein functional analysis.

eBioinformaticsResource Content

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This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.

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FASTR3DTool Content

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FASTR3D is a web based search tool that allows users to search the PDB database for structurally similar RNAs from input queries of PDB coordinates for an RNA molecule, an RNA secondary structure or RNA primary sequence.

FFASTool Content

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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.

links directory index: 271
TitlePublication YearGoogle Scholar Citation Count
FFAS03: a server for profile--profile sequence alignments2005271

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