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Sequence Comparison

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

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Found 17 links

Displaying 15 links

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@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.

NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

Bioinformatics ToolkitTool Content

http://toolkit.tuebingen.mpg.de/

DNA > Annotations
DNA > DNA and Genomic Analysis
DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Localization and Targeting
Protein > Molecular Dynamics and Docking
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

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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BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

NAR Web Server Issue 2005NAR Web Server Issue 2003
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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

COMATool Content

http://www.ibt.lt/bioinformatics/coma/

Protein > Sequence Comparison

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.

This content is being maintained by venc.

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tagsdistant homology detection profile-profile alignment sequence profile

d-OmixTool Content

http://www.biotec.or.th/isl/Domix

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

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.

NAR Web Server Issue 2009
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tagsphylogeny protein interaction domains and motifs proteins proteomics tertiary protein structure

HMMER Web ServerTool Content

http://hmmer.janelia.org

Protein > Sequence Comparison
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

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.

NAR Web Server Issue 2011
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HotSpot WizardTool Content

http://loschmidt.chemi.muni.cz/hotspotwizard/

Protein > Annotation and Function
Protein > Biochemical Features
Protein > Sequence Comparison
Protein > Sequence Features

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.

NAR Web Server Issue 2009
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tagsbeta-lactamases glycoside hydrolases hydrolases phosphoric triester hydrolases protein engineering reproducibility of results

InteroPORCTool Content

http://biodev.extra.cea.fr/interoporc/

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Comparison

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

http://www.cbs.dtu.dk/services/MaxAlign/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Other Alignment Tools

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.

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tagsalgorithms automated pattern recognition genetic databases sequence alignment sequence analysis

Multi-HarmonyTool Content

http://www.ibi.vu.nl/programs/shmrwww

Protein > Sequence Comparison
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

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.

NAR Web Server Issue 2010
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tagsalgorithms protein sequence analysis sequence alignment smad proteins

PLecDomTool Content

http://www.nipgr.res.in/plecdom.html

DNA > Phylogeny Reconstruction
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Model Organisms > Plants
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Pairwise Sequence Alignments

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.

NAR Web Server Issue 2009
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tagsmarkov chains plant lectins protein sequence analysis sequence alignment tertiary protein structure

PPISearchTool Content

http://gemdock.life.nctu.edu.tw/ppisearch/

Protein > Interactions, Pathways, Enzymes
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison
Sequence Comparison > Similarity Searching

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.

NAR Web Server Issue 2009
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tagsadaptor protein complex 1 amino acid sequence homology animals caenorhabditis elegans proteins mice protein databases protein interaction domains and motifs protein interaction mapping

ProGMapTool Content

http://www.bioinformatics.nl/progmap

Protein > Annotation and Function
Protein > Proteomics
Protein > Sequence Comparison

Protein Group Mappings (ProGMap) facilitates the annotation of newly sequenced proteins by helping users assess the coherence of protein groups found in various databases. ProGMap is based on a non-redundant dataset of over 6.6 million protein sequences mapped to 240,000 protein groups. Queries through ProGMap may be made using sequence identifiers, gene symbols, protein functions or amino acid sequences.

NAR Web Server Issue 2009
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tagsprotein databases protein sequence analysis proteins systems integration

SCANPSTool Content

http://www.compbio.dundee.ac.uk/www-scanps

Protein > Sequence Comparison
Sequence Comparison > Pairwise Sequence Alignments

SCANPS is a web server for iterative protein sequence database searching by dynamic programming. Sensitivity and selectivity outperform PSI-BLAST. The server allows a range of different protein sequence databases to be searched including the SCOP database of protein domains.

NAR Web Server Issue 2008
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tagsprotein databases protein sequence analysis sequence alignment tertiary protein structure

STING MilleniumTool Content

http://luna.bioc.columbia.edu/SMS/STINGm/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

NAR Web Server Issue 2003NAR Web Server Issue 2005
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tagsacid anhydride hydrolases algorithms alpha-amylases amino acid sequence amino acid sequence homology amino acids animals beetles binding sites chemical models chymotrypsin color computational biology computer simulation conserved sequence enzyme inhibitors fabaceae hiv integrase hydrogen bonding lectins medicinal plants molecular cloning molecular models molecular sequence data molecular structure online systems ovomucin plant lectins plant proteins proprotein convertases protein binding protein conformation protein databases protein interaction mapping protein sequence analysis protein structural homology proteins quaternary protein structure recombinant proteins sequence alignment structure-activity relationship systems integration x-ray crystallography

Tags associated with subcategory 'Protein/Sequence Comparison'

protein sequence analysis sequence alignment protein databases algorithms proteins molecular models protein interaction mapping protein structural homology tertiary protein structure protein conformation amino acid sequence homology animals lectins hiv integrase medicinal plants fabaceae hydrogen bonding computational biology enzyme inhibitors binding sites beetles amino acids chemical models chymotrypsin conserved sequence molecular cloning color plant lectins molecular sequence data computer simulation x-ray crystallography energy metabolism gene expression profiling proteomics proteome gene expression regulation systems integration structure-activity relationship ovomucin online systems molecular structure plant proteins proprotein convertases recombinant proteins quaternary protein structure protein binding united states signal transduction phosphoprotein phosphatases smad proteins sequence profile protein folding protein kinases glycoside hydrolases caenorhabditis elegans proteins membrane proteins transcription factors profile-profile alignment distant homology detection phylogeny beta-lactamases adaptor protein complex 1 ligands acid anhydride hydrolases chromosome mapping biological models amino acid sequence alpha-amylases hydrolases phosphoric triester hydrolases mice humans genome national library of medicine (u.s.) nucleic acid databases time factors statistical models sequence homology sensitivity and specificity expressed sequence tags dna genetic databases markov chains reproducibility of results protein engineering sequence analysis dimerization base sequence automated pattern recognition protein interaction domains and motifs multiprotein complexes