Sequence Comparison

The links from this subcategory have been moved. They are now located in Top : Sequence Comparison.

Found 21 links

Displaying 15 links

@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.

AlignMeTool Content

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AlignMe (for Alignment of Membrane Proteins) can be used to examine detailed similarity between homologous proteins even if there is no notable sequence similarity. The predefined gap/weight sets have been optimized for membrane proteins, and so should be particularly useful for these difficult cases.

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Alignment-AnnotatorTool Content

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Alignment Annotator is a web service which annotates and renders sequence alignments using annotation services and the PDB. The annotated and colorized alignment can be downloaded as an interactive HTML file for web browsers.

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Bioinformatics ToolkitTool Content

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This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

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BioShell ThreaderTool Content

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BioShell Threader is a webserver for protein homology detection. Homology detection is based on sequence profiles and secondary structure profiles.

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COMATool Content

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COMA is a distant homology detection method based on sequence profile–profile comparison. COMA takes a protein sequence or multiple sequence alignment as input and searches for remote homologs in SCOP, PDB and PFAM databases.

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d-OmixTool Content

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A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
d-Omix: a mixer of generic protein domain analysis tools20091

HMMER Web ServerTool Content

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HMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for searching a protein sequence against Pfam.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
HMMER web server: interactive sequence similarity searching201124

HotSpot WizardTool Content

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HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis are selected based on the integration of structural, functional and evolutionary information from various databases and tools.

InteroPORCTool Content

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InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for any species present in the Integr8 database (more than 1500 organisms). The method combines known interactions and clusters of orthologous proteins. The tool can be downloaded or used through the web application.

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MaxAlignTool Content

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MaxAlign is a web server for maximizing usable data in an alignment. It maximizes the number of nucleotide (or amino acid) symbols present in gap-free columns by selecting the optimal subset of sequences to exclude from the alignment.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
MaxAlign: maximizing usable data in an alignment20079

Multi-HarmonyTool Content

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Multi-Harmony is an interactive web server for detecting sub-type specific sites in proteins starting from a multiple sequence alignment. Combines Sequence Harmony and Multi-Relief methods.

PLecDomTool Content

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PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classes, estimate the extent of divergence of new domains, extract domain boundaries and examine flanking sequence.

PPISearchTool Content

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PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple species.

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