Genome-guided transcriptome assembly in the age of next-generation sequencing

Research output: Contribution to journalArticle

Abstract

Next generation sequencing technologies provide unprecedented power to explore the repertoire of genes and their alternative splice variants, collectively defining the transcriptome of a species in great detail. However, assembling the short reads into full-length gene and transcript models presents significant computational challenges. We review current algorithms for assembling transcripts and genes from next generation sequencing reads aligned to a reference genome, and lay out areas for future improvements.

Original languageEnglish (US)
Article number6654138
Pages (from-to)1234-1240
Number of pages7
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume10
Issue number5
DOIs
StatePublished - Sep 2013

Fingerprint

Transcriptome
Sequencing
Genome
Genes
Gene
Layout
Technology
Alternatives
Model

Keywords

  • Algorithms
  • Biology and genetics
  • Computer applications
  • Medicine and science

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Applied Mathematics
  • Medicine(all)

Cite this

@article{fdf23422350c4bd1864dac3d4667d525,
title = "Genome-guided transcriptome assembly in the age of next-generation sequencing",
abstract = "Next generation sequencing technologies provide unprecedented power to explore the repertoire of genes and their alternative splice variants, collectively defining the transcriptome of a species in great detail. However, assembling the short reads into full-length gene and transcript models presents significant computational challenges. We review current algorithms for assembling transcripts and genes from next generation sequencing reads aligned to a reference genome, and lay out areas for future improvements.",
keywords = "Algorithms, Biology and genetics, Computer applications, Medicine and science",
author = "Florea, {Liliana D} and Salzberg, {Steven L}",
year = "2013",
month = "9",
doi = "10.1109/TCBB.2013.140",
language = "English (US)",
volume = "10",
pages = "1234--1240",
journal = "IEEE/ACM Transactions on Computational Biology and Bioinformatics",
issn = "1545-5963",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
number = "5",

}

TY - JOUR

T1 - Genome-guided transcriptome assembly in the age of next-generation sequencing

AU - Florea, Liliana D

AU - Salzberg, Steven L

PY - 2013/9

Y1 - 2013/9

N2 - Next generation sequencing technologies provide unprecedented power to explore the repertoire of genes and their alternative splice variants, collectively defining the transcriptome of a species in great detail. However, assembling the short reads into full-length gene and transcript models presents significant computational challenges. We review current algorithms for assembling transcripts and genes from next generation sequencing reads aligned to a reference genome, and lay out areas for future improvements.

AB - Next generation sequencing technologies provide unprecedented power to explore the repertoire of genes and their alternative splice variants, collectively defining the transcriptome of a species in great detail. However, assembling the short reads into full-length gene and transcript models presents significant computational challenges. We review current algorithms for assembling transcripts and genes from next generation sequencing reads aligned to a reference genome, and lay out areas for future improvements.

KW - Algorithms

KW - Biology and genetics

KW - Computer applications

KW - Medicine and science

UR - http://www.scopus.com/inward/record.url?scp=84894560949&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84894560949&partnerID=8YFLogxK

U2 - 10.1109/TCBB.2013.140

DO - 10.1109/TCBB.2013.140

M3 - Article

C2 - 24524156

AN - SCOPUS:84894560949

VL - 10

SP - 1234

EP - 1240

JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics

JF - IEEE/ACM Transactions on Computational Biology and Bioinformatics

SN - 1545-5963

IS - 5

M1 - 6654138

ER -