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Links tagged with 'fungal genome'

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Found 28 links

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AmoebaDB and MicrosporidiaDBDatabase Content

http://AmoebaDB.org

Model Organisms > Databases

AmoebaDB and MicrosporidiaDB are functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. Search strategies can be saved within a user's profile for future retrieval and may also be shared with other researchers using a unique strategy web address.

NAR Database Issue 2011
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tagsencephalitozoon entamoeba fungal genome genetic databases genomics protozoan genome

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

BROPResource Content

http://brop.org/

Expression > Transcript Expression Analysis
Model Organisms > Microbes

The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.

NAR Web Server Issue 2005
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tagsbacteria bacterial capsules bacterial genes bacterial genome bacterial polysaccharides bacterial proteins biological evolution computational biology dna transposable elements fungal genome genetic databases genetic variation genomic islands genomics horizontal gene transfer integrases mouth oligonucleotide array sequence analysis open reading frames operon porphyromonas gingivalis sequence alignment streptococcus mutans transfer rna virulence virulence factors

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

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

CVTreeTool Content

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

Model Organisms > Microbes
Protein > Phylogeny Reconstruction

Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.

NAR Web Server Issue 2004NAR Web Server Issue 2009
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tagsalgorithms archaeal genome bacteria bacterial genome chloroplast dna fungal genome genome genomics phylogeny viral genome viruses

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

Ensembl Genome BrowserTool Content

http://www.ensembl.org/

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Model Organisms > Other Organisms

Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.

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tagsanimals bacterial genome base sequence cattle computational biology database management systems dna sequence analysis dogs fungal genome gene expression genetic databases genetic polymorphism genetic variation genome genomics human genome humans invertebrates mice nucleic acid databases nucleic acid regulatory sequences plant genome protein databases proteins rats reference standards rna sequence alignment species specificity synteny systems integration tertiary protein structure transcriptional regulatory elements

Ensembl GenomesDatabase Content

http://www.ensemblgenomes.org

Model Organisms > Databases

Ensembl Genomes is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

NAR Database Issue 2010
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tagsanimals anopheles gambiae bacterial genome classification computational biology fungal genome gene expression genetic databases genetic polymorphism genome humans invertebrates nucleic acid databases open reading frames plant genome search engine single nucleotide polymorphism tertiary protein structure

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

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

ITS2Tool Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/

DNA > Phylogeny Reconstruction
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

NAR Web Server Issue 2006
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tagsanimals base sequence computational biology conserved sequence eukaryota fungal genome fungi genetic databases genetic markers genetic transcription invertebrates molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny plant genome plants ribosomal rna ribosomal spacer dna rna sequence analysis sequence alignment tertiary protein structure

ITS2Database Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.pl?search

DNA > Databases

The ITS2 Database holds information about sequence, structure and taxonomic classification of all internal transcribed spacer 2 (ITS2) in GenBank. ITS2 can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs.

NAR Database Issue 2010
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tagsbase sequence computational biology fungal genome fungi genetic databases molecular sequence data nucleic acid databases nucleic acid sequence homology plant genome plants ribosomal spacer dna tertiary protein structure

Microbial Genome Database (MBGD)Database Content

http://mbgd.genome.ad.jp/

Model Organisms > Databases

The microbial genome database (MBGD) for comparative analysis is a platform for microbial comparative genomics based on automated ortholog group identification. A prominent feature of MBGD is that it allows users to create ortholog groups using a specified subgroup of organisms. Advanced functionalities include: (i) enhanced assignment of functional annotation, including external database links to each orthologous group, (ii) interface for choosing a set of genomes to compare based on phenotypic properties, (iii) the addition of more eukaryotic microbial genomes (fungi and protists) and some higher eukaryotes as references and (iv) enhancement of the MyMBGD mode, which allows users to add their own genomes to MBGD and now accepts raw genomic sequences without any annotation (in such a case, it runs a gene-finding procedure before identifying the orthologs).

NAR Database Issue 2010
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tagsanimals bacterial genome computational biology fungal genome genetic databases genomics humans nucleic acid databases phylogeny protein databases sequence alignment tertiary protein structure