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Links tagged with 'sequence homology'

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Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

E-RNAiTool Content

http://e-rnai.dkfz.de/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Fly
Model Organisms > Other Organisms
Model Organisms > Yeast
RNA > Structure Prediction, Visualization, and Design

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

NAR Web Server Issue 2005NAR Web Server Issue 2010
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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

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.

NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

euGenes: Genomic Information for Eukaryotic OrganismsDatabase Content

http://iubio.bio.indiana.edu:8089/

Model Organisms > General Resources

Summary of gene and genomic information automatically maintained from primary eukaryotic organism databases: gene symbol, full name, chromosome, genetic and molecular maps, gene products, links to extended gene information.

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tagsanimals arabidopsis caenorhabditis elegans chromosome mapping database management systems drosophila forecasting genetic databases genome humans mice saccharomyces sequence homology zebrafish

GObletTool Content

http://goblet.molgen.mpg.de/

Protein > Annotation and Function
Sequence Comparison > Analysis of Aligned Sequences

GOblet allows the user to BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for the group if more than one sequence is submitted.

NAR Web Server Issue 2004NAR Web Server Issue 2003
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tagsanimals complementary dna dna sequence analysis genes humans invertebrates mice plants protein databases protein sequence analysis proteins reproducibility of results sequence homology terminology as topic

ICGEBnet Protein ToolsTool Content

http://www.icgeb.org/protein/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

ICGEBnet Protein Tools is a resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) and/or depth (DPX) indexes in 3D models.

NAR Web Server Issue 2005
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tagsalgorithms animals chemical models cluster analysis computational biology crystallography humans interferon alfa-2a molecular evolution molecular models molecular structure probability programming languages protein conformation protein databases protein folding protein interaction mapping proteins secondary protein structure sensitivity and specificity sequence homology serpins tertiary protein structure trypsin

InParanoidDatabase Content

http://inparanoid.sbc.su.se/cgi-bin/index.cgi

Protein > Databases

The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters.

NAR Database Issue 2010
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tagsalgorithms animals bacterial genome cluster analysis computational biology database management systems escherichia coli eukaryotic cells gene duplication genetic databases genomics humans mice nucleic acid databases phylogeny protein databases proteins proteomics rats sequence homology tertiary protein structure

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/

Expression > Networks
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

NAR Web Server Issue 2008
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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

MIPSDatabase Content

http://mips.gsf.de/

Model Organisms > General Resources
Model Organisms > Other Organisms
Model Organisms > Plants
Model Organisms > Yeast
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, MPPI, SIMAP, QUIPOS, MATDB, MOsDB, SPUTNIK, and PEDANT.

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tagsanimals arabidopsis arabidopsis proteins biological models complementary dna computational biology dna transposable elements expressed sequence tags fungi gene duplication genetic databases genome genomics humans mice nucleic acid databases nucleic acid sequence homology oryza sativa plant genes plant genome protein binding protein databases protein interaction mapping protein sequence analysis proteins proteomics saccharomyces cerevisiae proteins sequence homology

ModellerTool Content

http://salilab.org/modeller/

Protein > 3-D Structure Prediction

Homology or comparative modeling of 3D protein structures.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology animals bacterial proteins biological models carrier proteins computer simulation enzymes factual databases genetic models genome genomics humans kallikreins l-lactate dehydrogenase mathematics molecular models molecular sequence data pancreatic elastase probability protein conformation protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure theoretical models thermodynamics tissue kallikreins trichomonas vaginalis trypsin

NCBI Map ViewerTool Content

http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi

DNA > Annotations
Human Genome > Annotations

The NCBI Map Viewer provides graphical displays of features on NCBI\'s assembly of human genomic sequence data as well as cytogenetic, genetic, physical, and radiation hybrid maps.

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tagsanimals biotechnology chromosome mapping gene expression profiling genes genetic databases genome humans mice molecular models phenotype sequence alignment sequence homology tertiary protein structure united states
setsNational Center for Biotechnology Information (NCBI)

PBILTool Content

http://pbil.univ-lyon1.fr/

Education > Directories and Portals

Pole Bio-Informatique Lyonnais (PBIL) provides access to sequence databanks (EMBL, GenBank, SWISS-PROT, PIR) and to many tools of nucleic acid and protein sequence analyses.

NAR Web Server Issue 2003
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tagsdna sequence analysis genetic databases molecular models nucleic acids protein conformation protein sequence analysis proteins rna sequence analysis secondary protein structure sequence alignment sequence homology systems integration

PhEVERDatabase Content

http://pbil.univ-lyon1.fr/databases/phever

Model Organisms > Databases

The PhEVER database provides accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers. It is a database of homologous families both (i) between sequences from different viruses and (ii) between viral sequences and sequences from cellular organisms. It offers a clustering of proteins into homologous families containing at least one viral sequences, as well as alignments and phylogenies for each of these families.

This content is being maintained by Leonor Palmeira.

NAR Database Issue 2011
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tagscluster analysis genetic databases genomics horizontal gene transfer host-pathogen interactions molecular evolution phylogeny sequence homology viral genes viral genome viral proteins viruses

Rat Genome Database (RGD)Database Content

http://rgd.mcw.edu/

Model Organisms > Mouse and Rat

The Rat Genome Database (RGD) is a repository of rat genetic and genomic data. As well as integrating this data with mapping, physiological and strain information, RGD also provides researchers with several tools that facilitate searching, data mining and data analysis.

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tagsanimal disease models animals cardiovascular diseases chromosome mapping database management systems disease genetic databases genetic markers genetic variation genome genomics genotype heritable quantitative trait humans inborn genetic diseases inbred strains rats mice microsatellite repeats nervous system diseases nucleic acid databases phenotype quantitative trait loci radiation hybrid mapping rats sequence homology signal transduction systems integration terminology as topic

RPBSResource Content

http://bioserv.rpbs.jussieu.fr/

Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Biochemical Features
Protein > Sequence Features

Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP).

This content is being maintained by jompo.

NAR Web Server Issue 2005
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tagsacquired immunodeficiency syndrome algorithms amino acid sequence amino acid sequence homology amino acids animals arabidopsis autoimmune diseases azurin bacterial genome chemical models computational biology computer simulation computer-assisted numerical analysis consensus sequence database management systems dna dna sequence analysis evaluation studies as topic factual databases genetic databases globins glycine hiv humans hydrolases leghemoglobin logistic models methods molecular models molecular sequence data nucleic acid sequence homology plant genome plastocyanin protein conformation protein structural homology proteins rats reproducibility of results secondary protein structure sequence alignment sequence analysis sequence homology solvents thiosulfate sulfurtransferase