Investigating genomic structure using changept: A Bayesian segmentation model
Genomes are composed of a wide variety of elements with distinct roles and characteristics. Some of these elements are well-characterised functional components such as protein-coding exons. Other elements play regulatory or structural roles, encode functional non-protein-coding RNAs, or perform some...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Elsevier
2014-07-01
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| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S200103701400018X |
| _version_ | 1819083868462907392 |
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| author | Manjula Algama Jonathan M. Keith |
| author_facet | Manjula Algama Jonathan M. Keith |
| author_sort | Manjula Algama |
| collection | DOAJ |
| description | Genomes are composed of a wide variety of elements with distinct roles and characteristics. Some of these elements are well-characterised functional components such as protein-coding exons. Other elements play regulatory or structural roles, encode functional non-protein-coding RNAs, or perform some other function yet to be characterised. Still others may have no functional importance, though they may nevertheless be of interest to biologists. One technique for investigating the composition of genomes is to segment sequences into compositionally homogenous blocks. This technique, known as ‘sequence segmentation’ or ‘change-point analysis’, is used to identify patterns of variation across genomes such as GC-rich and GC-poor regions, coding and non-coding regions, slowly evolving and rapidly evolving regions and many other types of variation. In this mini-review we outline many of the genome segmentation methods currently available and then focus on a Bayesian DNA segmentation algorithm, with examples of its various applications. |
| first_indexed | 2024-12-21T20:39:24Z |
| format | Article |
| id | doaj.art-d9d4e6d2b6a84b04bf0744f5d6be9bef |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-21T20:39:24Z |
| publishDate | 2014-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-d9d4e6d2b6a84b04bf0744f5d6be9bef2022-12-21T18:51:01ZengElsevierComputational and Structural Biotechnology Journal2001-03702014-07-01101710711510.1016/j.csbj.2014.08.003Investigating genomic structure using changept: A Bayesian segmentation modelManjula AlgamaJonathan M. KeithGenomes are composed of a wide variety of elements with distinct roles and characteristics. Some of these elements are well-characterised functional components such as protein-coding exons. Other elements play regulatory or structural roles, encode functional non-protein-coding RNAs, or perform some other function yet to be characterised. Still others may have no functional importance, though they may nevertheless be of interest to biologists. One technique for investigating the composition of genomes is to segment sequences into compositionally homogenous blocks. This technique, known as ‘sequence segmentation’ or ‘change-point analysis’, is used to identify patterns of variation across genomes such as GC-rich and GC-poor regions, coding and non-coding regions, slowly evolving and rapidly evolving regions and many other types of variation. In this mini-review we outline many of the genome segmentation methods currently available and then focus on a Bayesian DNA segmentation algorithm, with examples of its various applications.http://www.sciencedirect.com/science/article/pii/S200103701400018XSequence segmentationBayesian modellingGeneralised Gibbs samplerConservation levelsGC contentNon-coding RNA |
| spellingShingle | Manjula Algama Jonathan M. Keith Investigating genomic structure using changept: A Bayesian segmentation model Computational and Structural Biotechnology Journal Sequence segmentation Bayesian modelling Generalised Gibbs sampler Conservation levels GC content Non-coding RNA |
| title | Investigating genomic structure using changept: A Bayesian segmentation model |
| title_full | Investigating genomic structure using changept: A Bayesian segmentation model |
| title_fullStr | Investigating genomic structure using changept: A Bayesian segmentation model |
| title_full_unstemmed | Investigating genomic structure using changept: A Bayesian segmentation model |
| title_short | Investigating genomic structure using changept: A Bayesian segmentation model |
| title_sort | investigating genomic structure using changept a bayesian segmentation model |
| topic | Sequence segmentation Bayesian modelling Generalised Gibbs sampler Conservation levels GC content Non-coding RNA |
| url | http://www.sciencedirect.com/science/article/pii/S200103701400018X |
| work_keys_str_mv | AT manjulaalgama investigatinggenomicstructureusingchangeptabayesiansegmentationmodel AT jonathanmkeith investigatinggenomicstructureusingchangeptabayesiansegmentationmodel |