What is the <mds_ies_db>?

The <mds_ies_db> is a database that uses customized searches and dynamic charts to elucidate the extensive genome rearrangement process occurring in some species of ciliates.

Ciliates contain two types of nuclei, a somatic macronucleus (MAC) and a germline micronucleus (MIC), with distinct genomes. During conjugation the MAC is disintegrated, and the MIC undergoes genome editing which includes large-scale deletion and segment rearrangement to form a new MAC (see Ciliate Biology for further details).

The <mds_ies_db> contains annotations for the MIC segments that are retained in the newly formed MAC, called macronuclear destined segments (MDSs), and the sequences that are excised from the MIC, called internal eliminated segments (IESs). Additionally the database contains annotations for the portions of the MIC MDSs, called pointers, that overlap in the MAC, and may help to guide the recombination process.

Annotation of a rearrangement event requires sequencing of a ciliate's corresponding MAC and MIC loci. Currently, there are only two ciliate species with fully sequenced MAC and MIC genomes: Oxytricha trifallax and Tetrahymena thermophilia (see Citations). The scope of the <mds_ies_db> is expected to grow as more MIC genomes are sequenced.

Reference: J. Burns, D. Kukushkin, K. Lindblad, X. Chen, N. Jonoska, L. Landweber. <mds_ies_db>: A Database of Ciliate Genome Rearrangements. Nucleic Acids Res. 44:D1 (2015) pp. D703-D709. DOI: 10.1093/nar/gkv1190

What's New?
Major updates to the database and interface to accomodate the annotation pipeline implemented by SDRAP.
Statistics page added
Home page updated
Help page added
About us page added
Tetrahymena thermophila and Oxytricha trifallax MDS annotation of MIC uploaded
Tetrahymena thermophila MDS annotation of MAC uploaded
Quick sequence search added together with new naming convention
Oxytricha trifallax MDS annotation of MAC uploaded
Genoverse genome browser added
Sequence search added
Gene search added
Chromosome (Contig) search added
Oxytricha trifallax MAC and MIC gene information uploaded
Quick contig search added
Dynamic contig information page is now generated for each contig in the database
Tetrahymena thermophila MAC and MIC genomes uploaded
Added chord diagrams to contig display
Oxytricha trifallax MAC and MIC genomes uploaded
Additional Features
In addition to rearrangement annotations, the <mds_ies_db> also contains MAC and MIC
  • genome and proteome assemblies,
  • cross-references to external databases
for Oxytricha and Tetrahymena.

Start Searching:

Chromosome Search

Contig Search

Search for contigs by length or number of MDSs, genes, or matches to other contigs.
Gene Search

Gene Search

Search for contigs by gene description, expression, or domains.
Sequence Search

Sequence Search

Search for contigs by nucleotide or amino acid sequence.