Detection of microRNAs in color spaceCitation formats

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Detection of microRNAs in color space. / Marco, Antonio; Griffiths-Jones, Sam.

In: Bioinformatics, Vol. 28, No. 3, btr686, 02.2012, p. 318-323.

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Marco, A & Griffiths-Jones, S 2012, 'Detection of microRNAs in color space', Bioinformatics, vol. 28, no. 3, btr686, pp. 318-323. https://doi.org/10.1093/bioinformatics/btr686

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Marco, Antonio ; Griffiths-Jones, Sam. / Detection of microRNAs in color space. In: Bioinformatics. 2012 ; Vol. 28, No. 3. pp. 318-323.

Bibtex

@article{9ebff6fbcea04dc3a2f7dccaf3581f3c,
title = "Detection of microRNAs in color space",
abstract = "Motivation: Deep sequencing provides inexpensive opportunities to characterize the transcriptional diversity of known genomes. The AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data is a sequence of colors, where each color represents 2 nt and each nucleotide is represented by two consecutive colors. This strategy is purported to have several advantages, including increased ability to distinguish sequencing errors from polymorphisms. Several programs have been developed to map short reads to genomes in color space. However, a number of previously unexplored technical issues arise when using SOLiD technology to characterize microRNAs. Results: Here we explore these technical difficulties. First, since the sequenced reads are longer than the biological sequences, every read is expected to contain linker fragments. The color-calling error rate increases toward the 3' end of the read such that recognizing the linker sequence for removal becomes problematic. Second, mapping in color space may lead to the loss of the first nucleotide of each read. We propose a sequential trimming and mapping approach to map small RNAs. Using our strategy, we reanalyze three published insect small RNA deep sequencing datasets and characterize 22 new microRNAs. {\textcopyright} The Author(s) 2011. Published by Oxford University Press. All rights reserved.",
author = "Antonio Marco and Sam Griffiths-Jones",
year = "2012",
month = feb,
doi = "10.1093/bioinformatics/btr686",
language = "English",
volume = "28",
pages = "318--323",
journal = "Bioinformatics (Oxford, England)",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "3",

}

RIS

TY - JOUR

T1 - Detection of microRNAs in color space

AU - Marco, Antonio

AU - Griffiths-Jones, Sam

PY - 2012/2

Y1 - 2012/2

N2 - Motivation: Deep sequencing provides inexpensive opportunities to characterize the transcriptional diversity of known genomes. The AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data is a sequence of colors, where each color represents 2 nt and each nucleotide is represented by two consecutive colors. This strategy is purported to have several advantages, including increased ability to distinguish sequencing errors from polymorphisms. Several programs have been developed to map short reads to genomes in color space. However, a number of previously unexplored technical issues arise when using SOLiD technology to characterize microRNAs. Results: Here we explore these technical difficulties. First, since the sequenced reads are longer than the biological sequences, every read is expected to contain linker fragments. The color-calling error rate increases toward the 3' end of the read such that recognizing the linker sequence for removal becomes problematic. Second, mapping in color space may lead to the loss of the first nucleotide of each read. We propose a sequential trimming and mapping approach to map small RNAs. Using our strategy, we reanalyze three published insect small RNA deep sequencing datasets and characterize 22 new microRNAs. © The Author(s) 2011. Published by Oxford University Press. All rights reserved.

AB - Motivation: Deep sequencing provides inexpensive opportunities to characterize the transcriptional diversity of known genomes. The AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data is a sequence of colors, where each color represents 2 nt and each nucleotide is represented by two consecutive colors. This strategy is purported to have several advantages, including increased ability to distinguish sequencing errors from polymorphisms. Several programs have been developed to map short reads to genomes in color space. However, a number of previously unexplored technical issues arise when using SOLiD technology to characterize microRNAs. Results: Here we explore these technical difficulties. First, since the sequenced reads are longer than the biological sequences, every read is expected to contain linker fragments. The color-calling error rate increases toward the 3' end of the read such that recognizing the linker sequence for removal becomes problematic. Second, mapping in color space may lead to the loss of the first nucleotide of each read. We propose a sequential trimming and mapping approach to map small RNAs. Using our strategy, we reanalyze three published insect small RNA deep sequencing datasets and characterize 22 new microRNAs. © The Author(s) 2011. Published by Oxford University Press. All rights reserved.

U2 - 10.1093/bioinformatics/btr686

DO - 10.1093/bioinformatics/btr686

M3 - Article

C2 - 22171334

VL - 28

SP - 318

EP - 323

JO - Bioinformatics (Oxford, England)

JF - Bioinformatics (Oxford, England)

SN - 1367-4803

IS - 3

M1 - btr686

ER -