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Links tagged with 'fungal proteins'

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Found 16 links

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AspGDDatabase Content

http://www.aspergillusgenome.org/

Model Organisms > Databases

The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data.

NAR Database Issue 2010
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tagsaspergillus nidulans computational biology fungal genes fungal genome fungal proteins genetic databases genetic models genetics nucleic acid databases phenotype protein databases tertiary protein structure

CiFDatabase Content

http://www.fusariumdb.org/

Model Organisms > Databases

The Cyber infrastructure for Fusarium (CiF) consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. The FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them using multiple tools without requiring repeated copying-and-pasting of sequences.

NAR Database Issue 2011
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tagsfungal genome fungal proteins fusarium genetic databases genomics multigene family phylogeny systems integration

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

DIPDatabase Content

http://dip.doe-mbi.ucla.edu/

Protein > Interactions, Pathways, Enzymes

The Database of Interacting Proteins (DIP) allows users to search for interacting proteins. Results lists can be searched and/or visualized (statically or dynamically). Users can submit new protein-protein interactions and update database entries.

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tagsanimals bacterial proteins computational biology factual databases forecasting fungal proteins helicobacter pylori humans information services macromolecular substances molecular models precipitin tests protein binding protein databases proteins reproducibility of results tertiary protein structure two-hybrid system techniques

DRYGinDatabase Content

http://drygin.ccbr.utoronto.ca/

Model Organisms > Databases
Protein > Databases

DRYGIN (Data Repository of Yeast Genetic Interactions)-a web database system that provides a central platform for yeast genetic network analysis and visualization. DRYGIN searches SGA interactions and integrates other data sources, in order to associate the genetic interactions with pathway information, protein complexes, other binary genetic and physical interactions, and Gene Ontology functional annotation.

NAR Database Issue 2010
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tagscomputational biology fungal genes fungal genome fungal proteins genetic databases genetic models nucleic acid databases protein databases protein interaction mapping tertiary protein structure
setsUniversity of Toronto

FGDBDatabase Content

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

Model Organisms > Databases

The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database for Fusarium graminearum. The current version of FGDB v3.1 provides information on the full manually revised gene set based on the Broad Institute assembly FG3 genome sequence. The database serves as a convenient entry point to explore expression data results and to obtain information on the Affymetrix GeneChip probe sets.

This content is being maintained by ugueldener.

NAR Database Issue 2011
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tagsfungal genome fungal proteins fusarium gene expression profiling genetic databases molecular sequence annotation

HubbaTool Content

http://hub.iis.sinica.edu.tw/Hubba

Protein > Interactions, Pathways, Enzymes

Hub Objects Analyzer or Hubba is a web-based service for characterizing nodes of importance within a protein interactome data set.

NAR Web Server Issue 2008
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tagsalgorithms animals fungal proteins humans mice protein interaction mapping rats

JASPARDatabase Content

http://jaspar.cgb.ki.se

DNA > Databases
Expression > Databases

JASPAR is an open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. The database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family.

NAR Database Issue 2010
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tagsalgorithms animals chromatin immunoprecipitation computational biology fungal proteins genetic databases genome humans nucleic acid databases protein binding protein databases transcription factors

PipeAlignTool Content

http://bips.u-strasbg.fr/PipeAlign/

Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial proteins caenorhabditis elegans cluster analysis computational biology conserved sequence cytoplasmic and nuclear receptors factual databases fungal proteins gene expression profiling genetic transcription genomics haemophilus influenzae humans leukemia molecular sequence data phylogeny predictive value of tests protein databases protein sequence analysis proteins pyrococcus reproducibility of results saccharomyces cerevisiae sensitivity and specificity sequence alignment small nuclear ribonucleoproteins

Protein Dipole ServerTool Content

http://bioportal.weizmann.ac.il/dipol/

Protein > 3-D Structural Features
Protein > Biochemical Features

The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.

This content is being maintained by Clifford Felder.

NAR Web Server Issue 2007
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tagsbibliographic databases biophysics computational biology computer simulation enzymes fungal proteins mathematics molecular models protein conformation protein databases proteins secondary protein structure statistical models

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

S. pombe genomeDatabase Content

http://www.sanger.ac.uk/Projects/S_pombe/

Model Organisms > Yeast

Schizosaccharomyces pombe Genome Sequencing Project.

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tagsbase sequence centromere chromosome mapping dna sequence analysis eukaryotic cells fungal chromosomes fungal dna fungal genome fungal proteins gene duplication humans inborn genetic diseases introns schizosaccharomyces tertiary protein structure

ScansiteTool Content

http://scansite.mit.edu/

Protein > Domains and Motifs

Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains.

NAR Web Server Issue 2003
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tagsalgorithms amino acid motifs amino acid sequence animals binding sites cattle cdc2 protein kinase cdc2-cdc28 kinases computational biology consensus sequence cyclic amp-dependent protein kinases cyclin-dependent kinase 2 cyclin-dependent kinases factual databases fungal proteins genome humans mice mitogen-activated protein kinase kinases molecular models molecular sequence data molecular structure peptides phosphorylation protein binding protein conformation protein databases protein interaction mapping protein kinases protein sequence analysis protein-serine-threonine kinases proteins proteome rats saccharomyces cerevisiae proteins serine signal transduction substrate specificity tertiary protein structure threonine tyrosine

SGDDatabase Content

http://genome-www.stanford.edu/Saccharomyces/

Model Organisms > Yeast

The Saccharomyces Genome Database.

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tagsamino acid motifs amino acid sequence amino acid sequence homology animals base sequence bibliographic databases computational biology factual databases fungal genes fungal genome fungal proteins genetic databases humans molecular models molecular sequence data molecular weight nucleic acid sequence homology protein conformation protein databases saccharomyces cerevisiae saccharomyces cerevisiae proteins saccharomycetales sequence alignment sequence homology terminology as topic

The Mendel SiteTool Content

http://mendel.imp.ac.at/

Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting

The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.

NAR Web Server Issue 2003
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tagsacyltransferases amino acid motifs animals eukaryotic cells fungal proteins glycine glycosylphosphatidylinositols lipid metabolism molecular sequence data myristic acids peroxisomes plant proteins post-translational protein processing protein sequence analysis protein sorting signals proteins protozoan proteins viral proteins