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Links tagged with 'evaluation studies as topic'

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GRAMM-XTool Content

http://vakser.bioinformatics.ku.edu/resources/gramm/grammx

Protein > Molecular Dynamics and Docking

GRAMM-X is a protein docking server.

NAR Web Server Issue 2006
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tagsalgorithms antigen-antibody complex automation binding sites computational biology computer simulation dimerization evaluation studies as topic influenza virus hemagglutinin glycoproteins ligands macromolecular substances molecular conformation molecular models multiprotein complexes protein conformation protein databases protein folding protein interaction mapping protein structural homology proteomics reproducibility of results statistical models tertiary protein structure viral antibodies

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

NAR Web Server Issue 2003NAR Web Server Issue 2004
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

MLSTTool Content

http://www.mlst.net/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes.

NAR Web Server Issue 2005
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tagsalleles bacteria bacterial dna bacterial genes bacterial meningitis bacterial typing techniques cerebrospinal fluid cluster analysis dna sequence analysis evaluation studies as topic gene frequency humans meningococcal infections molecular sequence data mycological typing techniques neisseria meningitidis nucleic acid databases pneumococcal meningitis polymerase chain reaction serotyping streptococcus pneumoniae virulence

PSORT.orgTool Content

http://www.psort.org/

Protein > Localization and Targeting

PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence bacterial outer membrane proteins bacterial proteins bayes theorem binding sites cell membrane computational biology cytoplasm decision trees escherichia coli evaluation studies as topic expert systems factual databases fungal proteins gram-negative bacteria humans lipoproteins membrane proteins molecular sequence data neural networks (computer) protein databases protein precursors protein sequence analysis protein sorting signals proteins reproducibility of results saccharomyces cerevisiae secondary protein structure sequence alignment subcellular fractions

PubGeneTool Content

http://www.pubgene.org/

Expression > Gene Regulation
Literature > Text Mining and Semantics

Searchable literature network of human genes with tools for gene expression analysis. Choose from the free public service, or purchase the commercial package.

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tagsbibliographic databases database management systems evaluation studies as topic factual databases gene expression profiling gene expression regulation genetic models human genome humans medline oligonucleotide array sequence analysis

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

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

NAR Web Server Issue 2003NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

TRAMPLETool Content

http://gpcr.biocomp.unibo.it/biodec/

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.

NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial outer membrane proteins biological models chemical models computer security computer simulation database management systems double-blind method escherichia coli evaluation studies as topic factual databases forecasting haemophilus influenzae humans markov chains membrane proteins molecular models molecular sequence data neural networks (computer) porins protein folding protein sequence analysis protein sorting signals reproducibility of results rhodopseudomonas secondary protein structure sequence alignment software design statistical models

tRNAscan-SETool Content

http://lowelab.ucsc.edu/tRNAscan-SE/

RNA > Functional RNAs

tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Lowe Lab at UCSC)

NAR Web Server Issue 2005
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tagsanimals bacterial rna evaluation studies as topic factual databases genome genomics introns rna small nucleolar rna transfer rna