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Links tagged with 'fungal genes'

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Found 17 links

Displaying 15 links

antiSMASHTool Content

http://antismash.secondarymetabolites.org

DNA > Annotations
Model Organisms > Microbes
Sequence Comparison > Multiple Sequence Alignments

The antibiotic and Secondary Metabolite Analysis Shell (antiSMASH) is a resource for identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

NAR Web Server Issue 2011
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tagsbacteria bacterial genes bacterial genome biosynthetic pathways fungal genes fungal genome fungi genomics molecular sequence annotation peptide synthases polyketide synthases substrate specificity

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

Candida Genome DatabaseDatabase Content

http://www.candidagenome.org/

Model Organisms > Databases

The Candida Genome Database provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. Two tools have been added to the DB. The Biochemical Pathways tool provides visualization of metabolic pathways and analysis tools that facilitate interpretation of experimental data, including results of large-scale experiments, in the context of Candida metabolism. Textpresso for Candida allows searching through the full-text of Candida-specific literature, including clinical and epidemiological studies.

NAR Database Issue 2010
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tagscandida albicans computational biology fungal dna fungal genes fungal genome genetic databases nucleic acid databases open reading frames protein databases tertiary protein structure

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

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

Gene Set BuilderTool Content

http://www.cisreg.ca/gsb/

DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Human Genome > Other Resources
Model Organisms > General Resources
Protein > Sequence Retrieval

Gene Set Builder is a database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl database, which includes species from yeast to human. User-created information such as sets and customized annotations are stored and can be shared to facilitate easy access. Gene sets stored in the system can be exported in a variety of output formats - as lists of identifiers, in tables, or as sequences.

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tagscomputational biology database management systems factual databases fungal genes gene expression regulation genetic databases genome genomics humans programming languages

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

GeneTrailTool Content

http://genetrail.bioinf.uni-sb.de/index.php

DNA > Annotations
Expression > Transcript Expression Analysis
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting

GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.

NAR Web Server Issue 2007
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tagsanimals computational biology database management systems fungal genes gene expression regulation genetic databases genetic models genome genomics humans programming languages proteomics statistical models

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

ORESTTool Content

http://mips.gsf.de/genre/proj/orest/index.html

Expression > cDNA, EST, SAGE

Online Resource for EST (OREST) analysis is a EST analysis pipeline which allows rapid analysis of large amounts of ESTs or cDNAs from mammals and fungi. Functional annotation of the dataset is also included via either FunCat or GO annotation.

NAR Web Server Issue 2008
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tagsanimals chromosome mapping dna sequence analysis expressed sequence tags fungal genes humans mammals mice proteins rats saccharomyces cerevisiae

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

NAR Web Server Issue 2003NAR Web Server Issue 2008NAR Web Server Issue 2011
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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

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

SGDDatabase Content

http://www.yeastgenome.org/

Model Organisms > Databases

The Saccharomyces Genome Database (SGD) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae. The information in SGD includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary literature from which these data are derived. Phenotypes and genetic interaction data are also annotated and displayed in SGD.

This content is being maintained by yeastgenome.

NAR Database Issue 2010
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tagscomputational biology fungal dna fungal genes fungal genome genetic databases mutation nucleic acid databases phenotype protein databases saccharomyces cerevisiae tertiary protein structure

SiteSeerTool Content

http://rocky.bms.umist.ac.uk/SiteSeer/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.

NAR Web Server Issue 2003
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tags5' flanking region base sequence binding sites color dna sequence analysis fungal genes genetic promoter regions nucleic acid databases saccharomyces cerevisiae transcription factors