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Links tagged with 'eukaryotic cells'

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Found 24 links

Displaying 15 links

ARGOTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/argo/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.

NAR Web Server Issue 2005
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tagsalgorithms binding sites eukaryotic cells gene expression regulation genetic promoter regions genomics transcription factors

BIOBASE Gene Regulation databasesDatabase Content

http://www.gene-regulation.com/pub/databases.html

Protein > Interactions, Pathways, Enzymes

includes: TRANSFAC - transcription factor database; Patho DB - mutated forms of transcription factors and binding sites that are pathologically relevant; S/MARt DB - scaffold matrix transaction database; TRANSPATH - gene regulatory pathway database.

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tagsanimals binding sites chromatin chromosomes database management systems developmental gene expression regulation dna-binding proteins eukaryotic cells forecasting gene expression profiling gene expression regulation genetic databases genetic promoter regions genetic transcription humans macromolecular substances mice nuclear matrix nuclear proteins nucleic acid databases oligonucleotide array sequence analysis protein databases saccharomyces signal transduction systems integration tissue distribution transcription factors

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

ESLpredTool Content

http://www.imtech.res.in/raghava/eslpred/

Protein > Localization and Targeting

ESLpred is a tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.

This content is being maintained by raghavagps.

NAR Web Server Issue 2004
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tagsartificial intelligence dipeptides eukaryotic cells protein databases proteins reproducibility of results

EUGENE'HOMTool Content

http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl

DNA > Annotations
DNA > Gene Prediction
Model Organisms > Plants

EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.

NAR Web Server Issue 2003
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tagsalgorithms complementary dna dna sequence analysis eukaryotic cells genes genome initiator codon nucleic acid sequence homology plant dna rna splice sites

FrameDTool Content

http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD

DNA > Gene Prediction

FrameD is a program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts.

NAR Web Server Issue 2003
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tagsamino acid sequence homology bacterial genome complementary dna dna sequence analysis eukaryotic cells expressed sequence tags frameshift mutation gc rich sequence genes open reading frames

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

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

JASPARTool Content

http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

JASPAR is a non-redundant, curated collection of transcription factor binding profiles. Each profile is generated from published, experimentally defined eukaryotic transcription factor binding sites.

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tagsanimals base sequence binding sites computational biology dna eukaryotic cells genetic transcription humans molecular sequence data nucleic acid databases response elements transcription factors

Loc3DDatabase Content

http://cubic.bioc.columbia.edu/db/LOC3d/

Protein > Localization and Targeting

LOC3D is a database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence homology amino acids animals chloroplasts computational biology computer simulation eukaryotic cells humans neural networks (computer) nuclear localization signals plant proteins protein conformation protein databases protein sequence analysis protein transport proteins proteome reproducibility of results secondary protein structure sequence alignment subcellular fractions

LocalizomeTool Content

http://localodom.kobic.re.kr/LocaloDom/

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

Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information.

NAR Web Server Issue 2006
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tagscell compartmentation eukaryotic cells membrane proteins protein databases reproducibility of results secondary protein structure tertiary protein structure

LOCtargetTool Content

http://www.rostlab.org/services/LOCtarget/

Protein > Annotation and Function

LOCtarget is a tool for predicting, and a database of pre-computed predictions for, sub-cellular localization of eukaryotic and prokaryotic proteins. Several methods are employed to make the predictions, including text analysis of SWISS-PROT keywords, nuclear localization signals, and the use of neural networks.

NAR Web Server Issue 2004
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tagsamino acid sequence homology eukaryotic cells genetic databases genomics neural networks (computer) nuclear localization signals prokaryotic cells protein sequence analysis protein sorting signals proteins

MADAPTool Content

http://ccg.vital-it.ch/madap/

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations

MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).

NAR Web Server Issue 2007
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tagsalgorithms animals base sequence chromatin immunoprecipitation cluster analysis complementary dna computational biology dna primers eukaryotic cells expressed sequence tags genetic databases genetic promoter regions genome humans nucleic acid databases open reading frames response elements statistical models

MetaPath OnlineTool Content

http://scopes.biologie.hu-berlin.de/

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.

NAR Web Server Issue 2007
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tagsadenosine triphosphate algorithms animals archaea bacteria biological evolution biological models cell physiological phenomena chemical models coenzymes computational biology computer simulation energy metabolism eukaryotic cells factual databases gene expression profiling genetic models genetic variation glucose glycolysis humans inorganic chemicals kinetics metabolism molecular evolution nerve net organic chemicals phosphates phylogeny physiological adaptation protein biosynthesis proteins signal transduction species specificity substrate specificity

NetPhosTool Content

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

Protein > Sequence Features

NetPhos is a neural network-based method for predicting potential phosphorylation sites at serine, threonine or tyrosine residues in protein sequences

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tagsamino acid motifs amino acid sequence animals binding sites consensus sequence eukaryotic cells glycosylation molecular models neural networks (computer) nuclear proteins phosphoproteins phosphorylation phylogeny reproducibility of results sensitivity and specificity serine substrate specificity tertiary protein structure threonine trans-activators tyrosine