Deutsch
 
Hilfe Datenschutzhinweis Impressum
  DetailsucheBrowse

Datensatz

 
 
DownloadE-Mail
  RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements

Osipova, E., Hecker, N., & Hiller, M. (2019). RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements. GigaScience, 8(11): giz132. doi:10.1093/gigascience/giz132.

Item is

Basisdaten

einblenden: ausblenden:
Genre: Zeitschriftenartikel

Externe Referenzen

einblenden:

Urheber

einblenden:
ausblenden:
 Urheber:
Osipova, Ekaterina1, Autor           
Hecker, Nikolai1, Autor           
Hiller, Michael1, Autor           
Affiliations:
1Max Planck Institute for the Physics of Complex Systems, Max Planck Society, ou_2117288              

Inhalt

einblenden:
ausblenden:
Schlagwörter: -
 MPIPKS: Living matter
 Zusammenfassung: Background: Transposons and other repetitive sequences make up a large part of complex genomes. Repetitive sequences can be co-opted into a variety of functions and thus provide a source for evolutionary novelty. However, comprehensively detecting ancestral repeats that align between species is difficult because considering all repeat-overlapping seeds in alignment methods that rely on the seed-and-extend heuristic results in prohibitively high runtimes. Results: Here, we show that ignoring repeat-overlapping alignment seeds when aligning entire genomes misses numerous alignments between repetitive elements. We present a tool, RepeatFiller, that improves genome alignments by incorporating previously undetected local alignments between repetitive sequences. By applying RepeatFiller to genome alignments between human and 20 other representative mammals, we uncover between 22 and 84 Mb of previously undetected alignments that mostly overlap transposable elements. We further show that the increased alignment coverage improves the annotation of conserved non-exonic elements, both by discovering numerous novel transposon-derived elements that evolve under constraint and by removing thousands of elements that are not under constraint in placental mammals. Conclusions: RepeatFiller contributes to comprehensively aligning repetitive genomic regions, which facilitates studying transposon co-option and genome evolution.

Details

einblenden:
ausblenden:
Sprache(n):
 Datum: 2019-11-192019-11-01
 Publikationsstatus: Erschienen
 Seiten: -
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: -
 Identifikatoren: ISI: 000500759800002
DOI: 10.1093/gigascience/giz132
 Art des Abschluß: -

Veranstaltung

einblenden:

Entscheidung

einblenden:

Projektinformation

einblenden:

Quelle 1

einblenden:
ausblenden:
Titel: GigaScience
Genre der Quelle: Zeitschrift
 Urheber:
Affiliations:
Ort, Verlag, Ausgabe: London : BioMed Central
Seiten: - Band / Heft: 8 (11) Artikelnummer: giz132 Start- / Endseite: - Identifikator: ISSN: 2047-217X
CoNE: https://pure.mpg.de/cone/journals/resource/2047-217X