Emerging applications of read profiles towards the functional annotation of the genome

Functional annotation of the genome is important to understand the phenotypic complexity of various species. The road toward functional annotation involves several challenges ranging from experiments on individual molecules to large-scale analysis of high-throughput sequencing (HTS) data. HTS data i...

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Main Authors:	Pundhir, Sachin, Poirazi, Panayiota, Gorodkin, Jan
Format:	Online
Language:	English
Published:	Frontiers Media S.A. 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437211/

id	pubmed-4437211
recordtype	oai_dc
spelling	pubmed-44372112015-06-03 Emerging applications of read profiles towards the functional annotation of the genome Pundhir, Sachin Poirazi, Panayiota Gorodkin, Jan Genetics Functional annotation of the genome is important to understand the phenotypic complexity of various species. The road toward functional annotation involves several challenges ranging from experiments on individual molecules to large-scale analysis of high-throughput sequencing (HTS) data. HTS data is typically a result of the protocol designed to address specific research questions. The sequencing results in reads, which when mapped to a reference genome often leads to the formation of distinct patterns (read profiles). Interpretation of these read profiles is essential for their analysis in relation to the research question addressed. Several strategies have been employed at varying levels of abstraction ranging from a somewhat ad hoc to a more systematic analysis of read profiles. These include methods which can compare read profiles, e.g., from direct (non-sequence based) alignments to classification of patterns into functional groups. In this review, we highlight the emerging applications of read profiles for the annotation of non-coding RNA and cis-regulatory elements (CREs) such as enhancers and promoters. We also discuss the biological rationale behind their formation. Frontiers Media S.A. 2015-05-19 /pmc/articles/PMC4437211/ /pubmed/26042150 http://dx.doi.org/10.3389/fgene.2015.00188 Text en Copyright © 2015 Pundhir, Poirazi and Gorodkin. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Pundhir, Sachin Poirazi, Panayiota Gorodkin, Jan
spellingShingle	Pundhir, Sachin Poirazi, Panayiota Gorodkin, Jan Emerging applications of read profiles towards the functional annotation of the genome
author_facet	Pundhir, Sachin Poirazi, Panayiota Gorodkin, Jan
author_sort	Pundhir, Sachin
title	Emerging applications of read profiles towards the functional annotation of the genome
title_short	Emerging applications of read profiles towards the functional annotation of the genome
title_full	Emerging applications of read profiles towards the functional annotation of the genome
title_fullStr	Emerging applications of read profiles towards the functional annotation of the genome
title_full_unstemmed	Emerging applications of read profiles towards the functional annotation of the genome
title_sort	emerging applications of read profiles towards the functional annotation of the genome
description	Functional annotation of the genome is important to understand the phenotypic complexity of various species. The road toward functional annotation involves several challenges ranging from experiments on individual molecules to large-scale analysis of high-throughput sequencing (HTS) data. HTS data is typically a result of the protocol designed to address specific research questions. The sequencing results in reads, which when mapped to a reference genome often leads to the formation of distinct patterns (read profiles). Interpretation of these read profiles is essential for their analysis in relation to the research question addressed. Several strategies have been employed at varying levels of abstraction ranging from a somewhat ad hoc to a more systematic analysis of read profiles. These include methods which can compare read profiles, e.g., from direct (non-sequence based) alignments to classification of patterns into functional groups. In this review, we highlight the emerging applications of read profiles for the annotation of non-coding RNA and cis-regulatory elements (CREs) such as enhancers and promoters. We also discuss the biological rationale behind their formation.
publisher	Frontiers Media S.A.
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437211/
_version_	1613225466566541312

Emerging applications of read profiles towards the functional annotation of the genome

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