> Tag > Links tagged with 'eukaryotic cells'

Links tagged with 'eukaryotic cells'

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Found 25 links

Displaying 15 links

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ARGOTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/argo/ [open in a new window]

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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.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters200514
NAR Web Server Issue 2005
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tagsalgorithms binding sites eukaryotic cells gene expression regulation genetic promoter regions genomics transcription factors

BPROMPTTool Content

http://www.ddg-pharmfac.net/bprompt/BPROMPT/BPROMPT.html [open in a new window]

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

Bayesian PRediction Of Membrane Protein Topology (BPROMPT) uses a Bayesian Belief Network to combine the results of other membrane protein prediction methods for a protein sequence.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
BPROMPT: A consensus server for membrane protein prediction200337
NAR Web Server Issue 2003
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tagsbayes theorem eukaryotic cells membrane proteins prokaryotic cells protein sequence analysis reproducibility of results secondary protein structure

CompareProspectorTool Content

http://compareprospector.stanford.edu/ [open in a new window]

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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.

links directory index: 164
TitlePublication YearGoogle Scholar Citation Count
A suite of web-based programs to search for transcriptional regulatory motifs200432
Eukaryotic regulatory element conservation analysis and identification using comparative genomics2004132
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

ELMTool Content

http://elm.eu.org/ [open in a new window]

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Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.

links directory index: 1035
TitlePublication YearGoogle Scholar Citation Count
ELM--the database of eukaryotic linear motifs201215
ELM: the status of the 2010 eukaryotic linear motif resource201090
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
NAR Database Issue 2010NAR Web Server Issue 2003
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tagsamino acid motifs amino acid sequence amino acid sequence homology animals computational biology computer graphics disease eukaryota eukaryotic cells genetic databases humans information storage and retrieval internet molecular sequence data nucleic acid databases protein databases protein sequence analysis proteins software tertiary protein structure user-computer interface viral proteins

ELMTool Content

http://elm.eu.org/ [open in a new window]

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Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.

links directory index: 1035
TitlePublication YearGoogle Scholar Citation Count
ELM--the database of eukaryotic linear motifs201215
ELM: the status of the 2010 eukaryotic linear motif resource201090
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
NAR Database Issue 2010NAR Web Server Issue 2003
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external linksLink on Wikipedia
tagsamino acid motifs amino acid sequence amino acid sequence homology animals computational biology computer graphics disease eukaryota eukaryotic cells genetic databases humans information storage and retrieval internet molecular sequence data nucleic acid databases protein databases protein sequence analysis proteins software tertiary protein structure user-computer interface viral proteins

ESLpredTool Content

http://www.imtech.res.in/raghava/eslpred/ [open in a new window]

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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.

links directory index: 182
TitlePublication YearGoogle Scholar Citation Count
ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST2004182
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 [open in a new window]

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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.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences200337
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 [open in a new window]

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DNA > Gene Prediction

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

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences200364
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 [open in a new window]

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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.

links directory index: 714
TitlePublication YearGoogle Scholar Citation Count
The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update20044
The web server of IBM's Bioinformatics and Pattern Discovery group20039
Dictionary-driven prokaryotic gene finding200241
Dictionary-driven protein annotation200237
The emergence of pattern discovery techniques in computational biology200092
Building dictionaries of 1D and 3D motifs by mining the Unaligned 1D sequences of 17 archaeal and bacterial genomes.19990
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm1998531
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 [open in a new window]

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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.

links directory index: 612
TitlePublication YearGoogle Scholar Citation Count
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis201080
InParanoid 6: eukaryotic ortholog clusters with inparalogs2008127
Inparanoid: a comprehensive database of eukaryotic orthologs2005405
NAR Database Issue 2010
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external linksLink on Wikipedia
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 [open in a new window]

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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.

links directory index: 716
TitlePublication YearGoogle Scholar Citation Count
JASPAR: an open-access database for eukaryotic transcription factor binding profiles2004716
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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/ [open in a new window]

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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.

links directory index: 343
TitlePublication YearGoogle Scholar Citation Count
Mimicking cellular sorting improves prediction of subcellular localization2005234
Better prediction of sub-cellular localization by combining evolutionary and structural information200376
LOC3D: annotate sub-cellular localization for protein structures200333
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/ [open in a new window]

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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.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information200626
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/ [open in a new window]

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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.

links directory index: 36
TitlePublication YearGoogle Scholar Citation Count
LOCnet and LOCtarget: sub-cellular localization for structural genomics targets200436
NAR Web Server Issue 2004
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external linksLink on Twitter
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/ [open in a new window]

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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).

links directory index: 90
TitlePublication YearGoogle Scholar Citation Count
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data20075
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension200485
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

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