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Links tagged with 'protozoan genome'

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AmoebaDB and MicrosporidiaDBDatabase Content

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

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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.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species20118
NAR Database Issue 2011
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tagsencephalitozoon entamoeba fungal genome genetic databases genomics protozoan genome

dictyBase update 2011Database Content

http://www.dictybase.org [open in a new window]

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Model Organisms > Databases

dictyBase, the model organism database for Dictyostelium, provides well integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a 'reference genome' in the Amoebozoa clade. New features include ortholog display and the complete integration of the Dicty Stock Center with dictyBase.

This content is being maintained by rexchisholm.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa20116
NAR Database Issue 2011
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tagsamoebozoa dictyostelium genetic databases molecular sequence annotation protozoan genome protozoan proteins systems integration

EuPathDB (formerly ApiDB)Database Content

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

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Model Organisms > Databases

EuPathDB (formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. The EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. EuPathDB currently supports more than 80 searches. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
EuPathDB: a portal to eukaryotic pathogen databases201039
NAR Database Issue 2010
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tagsanimals computational biology genetic databases humans nucleic acid databases protein databases protozoan genome protozoan infections protozoan proteins tertiary protein structure

GeneFizzTool Content

http://pbga.pasteur.fr/GeneFizz/ [open in a new window]

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DNA > Gene Prediction

GeneFizz is a tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
GeneFizz: A web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives200322
Physics-based gene identification: proof of concept for Plasmodium falciparum200219
NAR Web Server Issue 2003
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tagsalgorithms animals biophysical phenomena biophysics computational biology dna dna sequence analysis drosophila melanogaster genes genetic code genetic models genetic techniques genomics molecular evolution nucleic acid conformation plasmodium falciparum protozoan dna protozoan genes protozoan genome

metaSHARKTool Content

http://bioinformatics.leeds.ac.uk/shark/ [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

Metabolic Search And Reconstruction Kit (metaSHARK) provides an interactive visualisation platform for the KEGG metabolic network in the form of the SHARKview applet.

links directory index: 74
TitlePublication YearGoogle Scholar Citation Count
metaSHARK: a WWW platform for interactive exploration of metabolic networks200611
metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella200563
NAR Web Server Issue 2006
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tagsanimals biological models coenzyme a dna sequence analysis eimeria tenella enzymes gene expression profiling genomics metabolism plasmodium falciparum protozoan genome

ParameciumDBDatabase Content

http://paramecium.cgm.cnrs-gif.fr [open in a new window]

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Model Organisms > Databases

ParameciumDB is a database built with the GMOD toolkit to integrate the genome and biology of the ciliate Paramecium tetraurelia. Post-genomic data from proteome and transcriptome studies has been incorporated along with predicted orthologs in 33 species, annotations from the community and publications from the scientific literature. Available tools include BioMart for complex queries, GBrowse2 for genome browsing, the Apollo genome editor for expert curation of gene models, a Blast server, a motif finder, and a wiki for protocols, nomenclature guidelines and other documentation. In-house tools have been developed for ontology browsing and evaluation of off-target RNAi matches.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia20114
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsgenetic databases genomics paramecium tetraurelia proteomics protozoan genome

TriTrypDBDatabase Content

http://www.TriTrypDB.org [open in a new window]

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Model Organisms > Databases

TriTrypDB is an integrated database providing access to genome-scale datasets for kinetoplastid parasites. TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a search strategy system that enables a user to construct complex queries combining multiple data types. 'User Comments' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
TriTrypDB: a functional genomic resource for the Trypanosomatidae201049
NAR Database Issue 2010
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tagsanimals computational biology genetic databases leishmania nucleic acid databases protein databases protozoan genome protozoan proteins tertiary protein structure trypanosoma

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