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Links tagged with 'saccharomyces cerevisiae'

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Found 48 links

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3D-partnerTool Content

http://3d-partner.life.nctu.edu.tw/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.

NAR Web Server Issue 2007
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tagsamino acid sequence amino acid sequence homology binding sites gene expression profiling molecular sequence data protein binding protein databases protein interaction mapping protein sequence analysis proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins tertiary protein structure

BioProspectorTool Content

http://robotics.stanford.edu/~xsliu/BioProspector/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.

NAR Web Server Issue 2004
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tagsalgorithms bacillus subtilis base sequence binding sites carrier proteins conserved sequence cyclic amp receptor protein dna escherichia coli gene expression profiling gene expression regulation genetic models genetic transcription markov chains nucleic acid regulatory sequences oligonucleotide array sequence analysis rap1 gtp-binding proteins regulator genes saccharomyces cerevisiae sequence alignment tata box transcription factors

COGsTool Content

http://www.ncbi.nlm.nih.gov/COG/

Protein > Domains and Motifs
Sequence Comparison > Comparative Genomics

Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.

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tagsamino acid sequence animals archaea archaeal genes archaeal proteins bacteria bacterial genes bacterial proteins caenorhabditis elegans conserved sequence drosophila melanogaster factual databases fungal genes fungal proteins genome methanococcus molecular evolution multigene family phylogeny proteins saccharomyces cerevisiae sequence alignment species specificity

CompareProspectorTool Content

http://compareprospector.stanford.edu/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.

NAR Web Server Issue 2004
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tagsalgorithms animals binding sites caenorhabditis caenorhabditis elegans conserved sequence dna eukaryotic cells fungal genes gene expression regulation genes genetic transcription genomics helminth genes humans mice nucleic acid regulatory sequences regulator genes saccharomyces saccharomyces cerevisiae schizosaccharomyces transcription factors

CORUMDatabase Content

http://mips.gsf.de/genre/proj/corum

Protein > Databases

CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). The CORUM dataset is built from 3198 different genes, representing approximately 16% of the protein coding genes in humans. Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. A 'Phylogenetic Conservation' analysis tool allows one to predict the occurrence of protein complexes in different phylogenetic groups.

NAR Database Issue 2010
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tagsanimals computational biology genetic databases humans mice multiprotein complexes phylogeny protein databases rats saccharomyces cerevisiae tertiary protein structure

DAnCERDatabase Content

http://wodaklab.org/dancer/

DNA > Databases

The DAnCER (Disease Annotated Chromatin Epigenetic Resource) resource integrates information on genes with chromatin modification (CM) function from five model organisms, including human. Currently integrated are gene functional annotations, Pfam domain architecture, protein interaction networks and associated human diseases. Additional supporting evidence includes orthology relationships across organisms, membership in protein complexes, and information on protein 3D structure. DAnCER allows visual explorations of the integrated data and flexible query capabilities using a variety of data filters. In particular, disease information and functional annotations are mapped onto the protein interaction networks.

NAR Database Issue 2011
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tagsanimals caenorhabditis elegans chromatin disease drosophila melanogaster epigenomics genetic databases humans mice molecular sequence annotation protein conformation protein interaction mapping saccharomyces cerevisiae

Gene2OligoTool Content

http://berry.engin.umich.edu/gene2oligo/

DNA > Tools For the Bench

Tool which divides both strands of an input DNA sequence into a set of contiguous oligonucleotides. These oligos are designed with complimentary regions so that the complete set can be combined to synthesize the input DNA sequence in vitro (using oligonucleotide synthesis and assembly PCR).

NAR Web Server Issue 2004
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tagsalgorithms cytochromes b5 dna ligases dna sequence analysis fungal genes nucleic acid hybridization oligonucleotides polymerase chain reaction saccharomyces cerevisiae temperature

INDELSCANTool Content

http://indelscan.genomics.sinica.edu.tw/IndelScan/

DNA > Annotations
Sequence Comparison > Analysis of Aligned Sequences

INDELSCAN is a tool for genome-wide identification of indels.

NAR Web Server Issue 2007
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tagsanimals base sequence computational biology genetic polymorphism human genome humans molecular sequence data mutation nucleic acid sequence homology saccharomyces cerevisiae sequence deletion single nucleotide polymorphism species specificity

Interolog/Regulog DatabaseDatabase Content

http://interolog.gersteinlab.org/

Model Organisms > Fly
Model Organisms > Plants
Model Organisms > Worm
Model Organisms > Yeast
Protein > Interactions, Pathways, Enzymes

Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.

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tagsamino acid sequence amino acid sequence homology animals bacterial dna bacterial genome bacterial proteins binding sites caenorhabditis elegans caenorhabditis elegans proteins computational biology conserved sequence dna dna-binding proteins drosophila melanogaster drosophila proteins fungal dna fungal genome genome helicobacter pylori helminth dna protein binding protein databases protein interaction mapping proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins

IsoBaseDatabase Content

http://isobase.csail.mit.edu/

Model Organisms > Databases
Protein > Databases

IsoBase is a database identifying functionally related proteins across five major eukaryotic model organisms: yeast, fly, worm, mouse, and human. Clusters were computed using the IsoRankN algorithm, which uses spectral methods, to combine sequence and PPI data to produce clusters of functionally related proteins. IsoBase may be browsed for functionally related proteins across two or more species and may also be queried by accession numbers, species-specific identifiers, gene name or keyword.

This content is being maintained by dkp.

NAR Database Issue 2011
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tagscaenorhabditis elegans cluster analysis drosophila melanogaster graph isomorphism graph spectral clustering humans interaction networks mice network alignment ortholog databases protein-protein interactions saccharomyces cerevisiae

LTR_FinderTool Content

http://tlife.fudan.edu.cn/ltr_finder/

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Model Organisms > Plants

LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.

NAR Web Server Issue 2007
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tagsalgorithms base sequence computational biology database management systems dna sequence analysis molecular sequence data nucleic acid databases retroelements saccharomyces cerevisiae sequence alignment terminal repeat sequences

MARQTool Content

http://marq.dacya.ucm.es

Expression > Gene Set Analysis
Expression > Transcript Expression Analysis

MARQ is a web based application that allows users to compare a query set of genes (query signature) against a gene signature database built from GEO datasets for different organisms and platforms.

NAR Web Server Issue 2010
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tagsanimals gene expression profiling genetic databases humans mice oligonucleotide array sequence analysis rats saccharomyces cerevisiae

MDscanTool Content

http://robotics.stanford.edu/~xsliu/MDscan/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.

This content is being maintained by brutlag.

NAR Web Server Issue 2004
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tagsalgorithms base sequence binding sites chromatin computational biology dna dna-binding proteins fungal genes gene expression regulation genetic transcription nucleic acid regulatory sequences oligonucleotide array sequence analysis precipitin tests protein binding response elements saccharomyces cerevisiae saccharomyces cerevisiae proteins sensitivity and specificity telomere telomere-binding proteins time factors transcription factors

MitoGenesisDBDatabase Content

http://www.dsimb.inserm.fr/dsimb_tools/mitgene/

Protein > Databases
RNA > Databases

MitoGenesisDB focuses on the dynamic of mitochondrial protein formation through global mRNA analyses. Three main parameters confer a global view of mitochondrial biogenesis: (i) time-course of mRNA production in highly synchronized yeast cell cultures, (ii) microarray analyses of mRNA localization that define translation sites and (iii) mRNA transcription rate and stability which characterize genes that are more dependent on post-transcriptional regulation processes. MitoGenesisDB integrates and establishes cross-comparisons between these data. Several model organisms can be analyzed via orthologous relationships between interspecies genes.

NAR Database Issue 2011
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tagsdata mining electron transport genetic transcription messenger rna mitochondria mitochondrial genes mitochondrial proteins protein biosynthesis protein databases rna stability saccharomyces cerevisiae saccharomyces cerevisiae proteins

mrepsTool Content

http://bioinfo.lifl.fr/mreps/

DNA > Structure and Sequence Feature Detection

mreps is a tool for identifing tandemn repeats in DNA sequences.

NAR Web Server Issue 2003
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tagsalgorithms bacterial dna bacterial genes dna dna sequence analysis genetic polymorphism genomics human genome humans neisseria meningitidis saccharomyces cerevisiae tandem repeat sequences