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ECRbase

http://ecrbase.dcode.org/

Description :
Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and Fugu genomes. It is freely accessible at http://ecrbase.dcode.org

Aknowledgement :
ECRbase was supported in part by grants from the Lawrence Livermore National Laboratory

References :
G.G. Loots and I. Ovcharenko, ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes, Bioinformatics, 23(1):122-4 (2007)

PeroxiBase

http://peroxibase.isb-sib.ch/index.php

Description :
Peroxidases from plants, bacteria and fungi

CFGP

http://cfgp.snu.ac.kr/

Description :
Comparative Fungal Genomics Platform

StrainInfo.net Bioportal

http://www.straininfo.net/

Description :
The StrainInfo.net Bioportal currently integrates data from 55 Biological Resource Centres (BRCs) that cover all earth s continents and range from small niche-specific research collections to large general-purpose service collections into an integrated strain database that underpins the Bioportal (Dawyndt et al., 2005). Information extracted from three taxonomic reference databases together with their type strains is incorporated as well. This integration process has currently lumped over 690,000 strain numbers into about 310,000 equivalence classes that represent different strains of Bacteria, Archaea, filamentous fungi, yeasts, Algae and Protozoa. Through the online interface of the StrainInfo.net Bioportal, organisms can be searched by strain number, taxonomic name (optionally restricted to type strains of these species), INSDC accession number, full text or combinations of the previous search parameters. Query results redirect the user on-the-fly to the online catalogues of the different culture collections that have a given strain that matches the query in their holdings. Additional pointers allow the user to navigate the downstream information available on these organisms, thereby rendering superfluous the need to browse a multitude of autonomous and heterogeneous information sources. For each organism, a list of all sequences deposited in the INSDC databases is given as a separate view. This overview is dynamically compiled irrespective of the strain numbers assigned to different cultures of the same organism during the sequence deposition process, solving possible Babel-like confusions. Sequence records are linked out to the corresponding records in the INSDC databases and the SILVA database. Similarly, another view assembles all scientific publications on a given organism, with links to the PubMed and DOI repositories whenever available. Finally, the integrated history and geographic views allow simple inspection of strain authenticity and availability.

References :
Dawyndt, P., Vancanneyt, M., De Meyer, H., Swings, J. (2005) Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources. IEEE Transactions on Knowledge and Data Engineering, 17(8), pp. 1111-1126.

OREST

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

Description :
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.

AHMII

http://www.wdcm.org/AHMII/ahmii.html

Description :
Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.

TIGR Fungal Gene Indices

http://www.tigr.org/tdb/tgi/fungi.shtml

Description :
Gene indicies for a number of fungal/yeast organisms such as Schizosaccharomyces pombe and Saccharomyces cerevisiae.

FGDB

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

Description :
Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two gene sets independently derived by automated annotation of the F.graminearum genome sequence. A complete manually revised gene set will be completed within the near future. The initial results of systematic manual correction of gene calls are already part of the current gene set. The database can be accessed to retrieve information from bioinformatics analyses and functional classifications of the proteins. The data are also organized in the well established MIPS catalogs and novel query techniques are available to search the data. The comprehensive set of gene calls was also used for the design of an Affymetrix GeneChip. The resource is accessible on http://mips.gsf.de/genre/proj/fusarium/.

Aknowledgement :
We thank Louise Riley for critical reading of the manuscript and the Fusarium research community for input on gene models and annotation details. This work was supported by the Austrian genome programme GEN-AU (bm:bwk Federal Ministry for Education, Science and Culture, GZ 200.051/6-VI/1/2001), the Impuls- und Vernetzungsfonds der Helmholtz-Gemeinschaft and a grant of the German Federal Ministry of Education and Research (BMBF) within the BFAM framework (031U112C/212C).

Fungal Genome Size Database

http://www.zbi.ee/fungal-genomesize/

Description :
Database of fungal genome size information has been launched in 2005: the Fungal Genome Size Database (http://www.zbi.ee/fungal-genomesize/). The database provides freely accessible genome size data assembled from literature. The taxonomy and the names of the used updated species follow Index Fungorum (http://www.indexfungorum.org). Genome size data are given as haploid (1C) values in megabases (Mb) and in picograms (pg).

The database offers flexible search facility. The data can be queried by different taxonomical levels (phylum, order, genus, species epithet, variety) as well as by ploidy level, chromosome number, chromosome size range, method of genome size estimation, standard specimens used, cell type analyzed, and source reference. Responses to queries are presented as tables, with detailed information about given records (e.g., herbarium index, original reference, and additional remarks) provided in a separate pop-up window accessed by clicking on a given genus or species name in the main table. Such data are of significant importance to the genomics community both as fundamental features of genome structure and as direct estimators of the cost of complete sequencing programs.

Recent develoments :
The current version of Fungal Genome Size Database (of 08 October 2006) includes 1,298 records covering 739 species from 40 orders and 335 genera.

Aknowledgement :
Fungal Genome Size Database is supported by grant no. 4989 from the Estonian Science Foundation.

References :
1. Gregory, T.R., Nicol, J.A., Tamm, H.; Kullman, B., Kullman, K., Leitch, I.J., Murray, B.G., Kapraun, D.F., Greilhuber, J., Bennett, M.D. (2007) Eukaryotic genome size databases. Nucleic Acids Research 35: in press.

DPVweb

http://www.dpvweb.net/

Description :
DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences are provided. The database also holds detailed, curated, information for all sequences of viruses, viroids and satellites of plants, fungi and protozoa that are complete or that contain at least one complete gene (currently, n~9000). For comparative purposes, it also contains a single representative sequence of all other fully sequenced virus species with an RNA or ssDNA genome. The start and end positions of each feature (gene, non-translated region, etc) have been recorded and checked for accuracy. As far as possible, nomenclature for genes and proteins are standardised within genera and families. Sequences of features (either as DNA or amino acid sequences) can be directly downloaded from the web site in FASTA format. The sequence information can also be accessed via client software for PC computers (freely downloadable from the web site) that enable users to make an easy selection of sequences and features of a chosen virus for further analyses.

Aknowledgement :
We thank the Association of Applied Biologists for their support, in particular by funding the development of the standalone DPV program and for sponsoring the DPVweb internet site. Rothamsted Research receives grant-aided support from the Biotechnology and Biological Sciences Research Council of the United Kingdom.

COGEME Phytopathogenic Fungi and Oomycete EST Database

http://cogeme.ex.ac.uk/

Description :
The COGEME phytopathogen EST database currently contains expressed sequence tags (ESTs) from eleven species of phytopathogenic fungi and two oomycete species. In order to reduce sequence redundancy, sequence assembly software was used to join together ESTs representing the same gene into a single contig or unisequence. Unisequences have been annotated based on similarity to known sequences and assigned to a functional classification group. The database can be queried by simple text queries against annotation, by functional classification, by similarity to known genes from Saccharomyces cerevisiae and using BLAST algorithms. Unisequence datasets can be downloaded. The database also contains an analysis of transcript abundance in Magnaporthe grisea and a demonstration of the use of EST data to predict the presence of amino acid pathways in different organisms. The database is described in Soanes et al. (2002).

Recent develoments :
The number of unisequences available in the database will increase as more ESTs become available. Transcriptomic data will also be added in the future.

Aknowledgement :
This work was supported by the Biotechnology and Biological Sciences COGEME project, part of the Investigating Gene Function Initiative.

References :
1. Soanes DM, Skinner W, Keon J, Hargreaves J, Talbot NJ (2002). Mol Plant Microbe Interact. 15(5): 421-427

PHI-base

http://www4.rothamsted.bbsrc.ac.uk/phibase/

Description :
To utilise effectively the growing number of verified genes that mediate an organismís ability to cause disease and / or to trigger host responses, we have developed PHI-base. This is a web-accessible database that currently catalogues 405 experimentally verified pathogenicity, virulence and effector genes from 54 fungal and Oomycete pathogens, of which 176 are from animal pathogens, 227 from plant pathogens and 3 from pathogens with a fungal host. PHI-base is the first on-line resource devoted to the identification and presentation of information on fungal and Oomycete pathogenicity genes and their host interactions. As such, PHI-base is a valuable resource for the discovery of candidate targets in medically and agronomically important fungal and Oomycete pathogens for intervention with synthetic chemistries and natural products. Each entry in PHI-base is curated by domain experts and supported by strong experimental evidence (gene / transcript disruption experiments) as well as literature references in which the experiments are described. Each gene in PHI-base is presented with its nucleotide and deduced amino acid sequence as well as a detailed description of predicted proteinís function during the host infection process. To facilitate data interoperability, we have annotated genes using controlled vocabularies (Gene Ontology terms, EC Numbers, etc.), and provide links to other external data sources (for example, NCBI taxonomy and EMBL). We welcome new data for inclusion in PHI-base, which is freely accessed at: www4.rothamsted.bbsrc.ac.uk/phibase/.

TargetIdentifier

https://fungalgenome.concordia.ca/tools/TargetIdentifier.html

Description :
TargetIdentifier is designed for identifying full-length EST cDNAs and functionally annotating EST cDNAs.

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