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
- 2021-12-20
- Major updates to the database and interface to accomodate the annotation pipeline implemented by SDRAP.
- 2015-09-06
- Statistics page added
- 2015-08-11
- Home page updated
- 2015-08-05
- Help page added
- 2015-08-01
- About us page added
- 2015-07-20
- Tetrahymena thermophila and Oxytricha trifallax MDS annotation of MIC uploaded
- 2015-07-11
- Tetrahymena thermophila MDS annotation of MAC uploaded
- 2015-07-04
- Quick sequence search added together with new naming convention
- 2015-06-24
- Oxytricha trifallax MDS annotation of MAC uploaded
- 2015-06-03
- Genoverse genome browser added
- 2015-05-10
- Sequence search added
- 2015-04-26
- Gene search added
- 2015-04-12
- Chromosome (Contig) search added
- 2015-03-09
- Oxytricha trifallax MAC and MIC gene information uploaded
- 2015-02-14
- Quick contig search added
- 2015-01-18
- Dynamic contig information page is now generated for each contig in the database
- 2014-11-21
- Tetrahymena thermophila MAC and MIC genomes uploaded
- 2014-11-15
- Added chord diagrams to contig display
- 2014-11-15
- Oxytricha trifallax MAC and MIC genomes uploaded
- genome and proteome assemblies,
- cross-references to external databases
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