BioHealthBase.org

Microsporidia

Research Center 1 for Microsporidia
Organism:

Microsporidia

Species:

The goal is to make the genome sequence of Nosema locustae rapidly and broadly available.

Center’s web site:
Sequencing Center:

Marine Biological Laboratory

Contacts at the sequence center:

Hilary Morrison at Morrison@mbl.edu

Related web link:

None

Assembly status:
  • The assembly contig consensus sequences will be posted on the web site. The researchers will continue to post the contigs-in-progress, Use the following link to view the current status and coverage of assembly: http://jbpc.mbl.edu/Nosema/Nannotation.html
Trace file:

Not available

Computational annotation status:

Nosema Locustae Genome Project Blast Server is at http://jbpc.mbl.edu/Nosema/Nblastcontig.html

Manual curation status:

Unknown

Research Center 2 for Microsporidia
Organism:

Microsporidia

Species:

Vittaforma corneae

Paper Information:
Sequencing status:

Seventy-four genome survey sequences (GSS) were obtained from genomic DNA of spores of laboratory-cultured V. corneae. Approximately, 41 discontinuous kilobases of V. corneae were cloned and sequenced to generate these GSS

Sequencing Center:

Unknown

Contacts at the sequence center:

Paul J at “Unknown address”

Relevant web link:

None

Assembly status:

Unknown

Trace file:

Not available

Computational annotation status:

BLASTX searches have been done for some of the putative genes and representativeproteins have been identified.

Manual curation status:

Unknown

Research Center 3 for Microsporidia
Organism:

Microsporidia

Species:

Encephalitozoon cuniculi

Genomic sequence status:
  • DNA sequences of the 11 chromosomes of the 2.9-megabase (Mb) genome of Encephalitozoon cuniculi (1,997 potential protein-coding genes) has been reported
  • Sequences of individual chromosomes were submitted to EMBL under the accession numbers AL39173 for chrI and AL590442–AL590451 for chrII–chrXI, respectively.
  • Supplementary information for genome sequence and gene compaction of Encephalitozoon cuniculi is also available: http://www.nature.com/nature/journal/v414/n6862/extref/414450aa.html
Paper’s web site:

“Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi”, Nature 414, 450 – 453 (22 November 2001); doi:10.1038/35106579

Sequencing Center:

University Blasise Pascal

Contacts at the sequence center:

Christian P. Vivares at christian.vivares@lbp.univ-bpclermont.fr

Related web link:

“Peyret, P. et al. Sequence and analysis of chromosome I of the amitochondriate intracellular parasite Encephalitozoon cuniculi (Microspora)”. Genome Res.11, 198-207 (2001).

Assembly status:

Should be finished

Trace file:

Not available

Computational annotation status:

Unknown

Manual curation status:

Annotation was manually performed.

Useful Research web sites for Microsporidia:

Genome Altas Database

  • Content:
    • The DNA Structural Atlas is a method of visualising structural features within large regions of DNA. It was originally designed for analysis of complete genomes, but can also be used quite readily for analysis of regions of DNA as small as a few thousand bp in length. The basic idea is to plot the values for six different mechanical-structural properties of the DNA helix in a circle (or arc) representing the complete genome (or chromosome). At the level of whole genomes or chromosomes, large architecturally important regions can be seen. At the level of individual genes (e.g., usually around 10,000 to 20,000 bp for the entire plot), intergenic regions can be examined. The plots are created using the “GeneWiz” program, developed by Hans-Henrik Stærfeldt here at CBS. A plot similar to the one shown below (for the complete genome of Escherichia coli can be automatically generated from a GenBank sequence file.

Protein of Encephalitozoon cuniculi Database:

  • Contact:
    • Research center: The University of California at San Diego
    • Email: wilfred@sdsc.edu
  • Content:
    • Proteins of Encephalitozoon cuniculi database is a part of the Encyclopedia of Life (EOL) project to predict the three dimensional structures of proteins encoded in all known genomes using an integrative genome annotation pipeline (iGAP) running on distributed resources.
  • Annotation strategy:
    • Proteins of Encephalitozoon cuniculi database provides a domain-based fold assignment to the Encephalitozoon cuniculi genome. The domains are based on SCOP classifications, using sequences specified by Astral. Additional domains are also included from PDP, as well as PDB chains not present in SCOP classifications.
  • Current release:
    • First public release 1/10/2003. The database contains 1,922 proteins from NCBI Genbank after clustering at the 100% sequence similarity level, bypassing sequences less than 30 amino acids in length (number of sequences downloaded from NCBI prior to clustering was 4,034)

Karolinska Institutet:

    • Paper information:
      • “Homeobox genes of Encephalitozoon cuniculis (Microsporidia) reveal a putative mating-type locus”, Development Genes Evolution, 2003, 21-50-52
      • http://springlink.metapress.com/media

Encephalitozoon cuniculiis (a parasite that belongs to a group of microsporidia)

  • Contact:
  • Content:
    • Proteins of Encephalitozoon cuniculi database is a part of the Encyclopedia of Life (EOL) project to predict the three dimensional structures of proteins encoded in all known genomes using an integrative genome annotation pipeline (iGAP) running on distributed resources.
  • Annotation strategy:
    • Proteins of Encephalitozoon cuniculi database provides a domain based fold assignment to the Encephalitozoon cuniculi genome. The domains are based on SCOP classifications, using sequences specified by Astral. Additional domains are also included from PDP, as well as PDB chains not present in SCOP classifications.
  • Current release:
    • First public release 1/10/2003. The database contains 1,922 proteins from NCBI Genbank after clustering at the 100% sequence similarity level, bypassing sequences less than 30 amino acids in length (number of sequences downloaded from NCBI prior to clustering was 4,034)