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Detection of microRNAs in color space.

Λεπτομέρειες βιβλιογραφικής εγγραφής
Τίτλος: Detection of microRNAs in color space.
Συγγραφείς: Marco, Antonio, Griffiths-Jones, Sam
Πηγή: Bioinformatics; Feb2012, Vol. 28 Issue 3, p318-323, 6p
Θεματικοί όροι: RNA analysis, Color, Nucleotide sequence, Linkers (Computer programs), Genetic transcription, Genetic polymorphisms, Computational biology
Περίληψη: 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.Availability and implementation: A bash shell script to perform the sequential trimming and mapping procedure, called SeqTrimMap, is available at: http://www.mirbase.org/tools/seqtrimmap/Contact: antonio.marco@manchester.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM PUBLISHER]
Copyright of Bioinformatics is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Detection of microRNAs in color space.
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  Data: <searchLink fieldCode="AR" term="%22Marco%2C+Antonio%22">Marco, Antonio</searchLink><br /><searchLink fieldCode="AR" term="%22Griffiths-Jones%2C+Sam%22">Griffiths-Jones, Sam</searchLink>
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  Data: Bioinformatics; Feb2012, Vol. 28 Issue 3, p318-323, 6p
– Name: Subject
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  Data: <searchLink fieldCode="DE" term="%22RNA+analysis%22">RNA analysis</searchLink><br /><searchLink fieldCode="DE" term="%22Color%22">Color</searchLink><br /><searchLink fieldCode="DE" term="%22Nucleotide+sequence%22">Nucleotide sequence</searchLink><br /><searchLink fieldCode="DE" term="%22Linkers+%28Computer+programs%29%22">Linkers (Computer programs)</searchLink><br /><searchLink fieldCode="DE" term="%22Genetic+transcription%22">Genetic transcription</searchLink><br /><searchLink fieldCode="DE" term="%22Genetic+polymorphisms%22">Genetic polymorphisms</searchLink><br /><searchLink fieldCode="DE" term="%22Computational+biology%22">Computational biology</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: 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.Availability and implementation: A bash shell script to perform the sequential trimming and mapping procedure, called SeqTrimMap, is available at: http://www.mirbase.org/tools/seqtrimmap/Contact: antonio.marco@manchester.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM PUBLISHER]
– Name: Abstract
  Label:
  Group: Ab
  Data: <i>Copyright of Bioinformatics is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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      – Type: doi
        Value: 10.1093/bioinformatics/btr686
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      – Code: eng
        Text: English
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        PageCount: 6
        StartPage: 318
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      – SubjectFull: RNA analysis
        Type: general
      – SubjectFull: Color
        Type: general
      – SubjectFull: Nucleotide sequence
        Type: general
      – SubjectFull: Linkers (Computer programs)
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      – SubjectFull: Genetic transcription
        Type: general
      – SubjectFull: Genetic polymorphisms
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      – SubjectFull: Computational biology
        Type: general
    Titles:
      – TitleFull: Detection of microRNAs in color space.
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              Text: Feb2012
              Type: published
              Y: 2012
          Identifiers:
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              Value: 28
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