Computational identification of transposable elements in the mouse genome

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dc.contributor.authorJjingo, Daudi
dc.contributor.authorMakalowski, Wojciech
dc.date.accessioned2018-07-20T12:48:41Z
dc.date.accessioned2021-12-21T08:58:57Z
dc.date.available2018-07-20T12:48:41Z
dc.date.available2021-12-21T08:58:57Z
dc.date.issued2007
dc.description.abstractRepeat sequences cover about 39 percent of the mouse genome and completion of sequencing of the mouse genome [1] has enabled extensive research on the role of repeat sequences in mammalian genomics. This research covers the identification of Transposable elements (TEs) within the mouse transcriptome, based on available sequence information on mouse cDNAs (complementary DNAs) from GenBank [28]. The transcripts are screened for repeats using RepeatMasker [23], whose results are sieved to retain only Interspersed repeats (IRS). Using various bioinformatics software tools as well as tailor made programming, the research establishes: (i) the absolute location coordinates of the TEs on the transcript. (ii) The location of the IRs with respect to the 5’UTR, CDS and 3’UTR sequence features. (iii) The quality of alignment of the TE’s consensus sequence on the transcripts where they exist, (iv) the frequencies and distributions of the TEs on the cDNAs, (v) descriptions of the types and roles of transcripts containing TEs. This information has been collated and stored in a relational database (MTEDB) at http://warta.bio.psu.edu/htt_doc/M TEDB/homepage.htm).en_US
dc.identifier.urihttps://hdl.handle.net/20.500.11951/253
dc.subjectMouse genomeen_US
dc.subjectTransposable elements, Geneticsen_US
dc.subjectMammalian genomicsen_US
dc.titleComputational identification of transposable elements in the mouse genomeen_US
dc.typeBook chapteren_US
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