Alignment Editing and Visualization

Tools for viewing, coloring, and editing sequence alignments.

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@TOME-2Tool Content

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@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

ALGGENTool Content

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ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

enoLOGOSTool Content

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enoLOGOS creates sequence logos based on a variety of input, including sequence alignments, probability and alignment matrices and energy measurements.

Enrichment Map Cytoscape PluginTool Content

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A Cytoscape plugin for functional enrichment visualization. Gene-sets, such as pathways and Gene Ontology terms, are organized into a network (i.e. the "enrichment map"). In this way, mutually overlapping gene-sets cluster together, making interpretation easier. Enrichment Map also enables the comparison of two different enrichment results in the same map.

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GeneDocTool Content

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Multiple sequence alignment editor, analyser and shading utility for Windows.

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LigAlignTool Content

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LigAlign: an automated system and structure visualization tool for flexible ligand alignment and analysis. When performing rigid alignments, LigAlign produces results consistent with manually annotated structural motifs. In performing flexible alignments, LigAlign automatically produces biochemically reasonable ligand fragmentations and subsequently identifies conserved structural motifs that are not detected by rigid alignment.

MapViewTool Content

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An information-rich short reads alignment viewer with genetic detection capability for next-generation sequencing technologies. MapView supports a compact alignment view for both single-end and pair-end short reads, multiple navigation and zoom modes, and multi-thread processing. MapView offers automated genetic variation detection.

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