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Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences
Joint Authors
Bachar, Dipankar
Guillou, Laure
Christen, Richard
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-12, 12 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-02-06
Country of Publication
Egypt
No. of Pages
12
Main Subjects
Abstract EN
The gene encoding SSU-rRNA sequences is the tool of choice for phylogenetic analyses and environmental biodiversity analyses of bacteria, Archaea but also unicellular Eukaryota.
In Eukaryota, gene sequences may often be interrupted by long or several introns.
Searching in GenBank release 188, we found descriptions of 3638 such sequences.
Using a database of 180 000 SSU-rRNA sequences well annotated for taxonomy and a C++ program written for that purpose, we computed the presence of 18 691 introns (among which the 3638 described introns).
Filtering on length and sequence quality, 3646 sequences were retained.
These introns were clustered; clusters were analyzed for the presence of single or multiple clades at various levels of taxonomic depth, allowing future analyses of horizontal transfers.
Various analyses of the results are provided as tabulated files as well as FASTA files of described or computed introns.
Each sequence is annotated for cellular location (nuclear, chloroplast, and mitochondria), positions at which they were found in the SSU-rRNA sequences and taxonomy as provided by GenBank.
American Psychological Association (APA)
Bachar, Dipankar& Guillou, Laure& Christen, Richard. 2013. Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences. Dataset Papers in Biology،Vol. 2013, no. 2013, pp.1-12.
https://search.emarefa.net/detail/BIM-503668
Modern Language Association (MLA)
Bachar, Dipankar…[et al.]. Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences. Dataset Papers in Biology No. 2013 (2013), pp.1-12.
https://search.emarefa.net/detail/BIM-503668
American Medical Association (AMA)
Bachar, Dipankar& Guillou, Laure& Christen, Richard. Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences. Dataset Papers in Biology. 2013. Vol. 2013, no. 2013, pp.1-12.
https://search.emarefa.net/detail/BIM-503668
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-503668