Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications

Summary: Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of ‘color space’, and it maximizes usable data b...

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Detalles Bibliográficos
Autores principales: Ondov, Brian D., Varadarajan, Anjana, Passalacqua, Karla D., Bergman, Nicholas H.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639273/
https://www.ncbi.nlm.nih.gov/pubmed/18842598
http://dx.doi.org/10.1093/bioinformatics/btn512
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author Ondov, Brian D.
Varadarajan, Anjana
Passalacqua, Karla D.
Bergman, Nicholas H.
author_facet Ondov, Brian D.
Varadarajan, Anjana
Passalacqua, Karla D.
Bergman, Nicholas H.
author_sort Ondov, Brian D.
collection PubMed
description Summary: Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of ‘color space’, and it maximizes usable data by allowing a user-specified number of mismatches. Sequence census functions facilitate a variety of functional genomics applications, including transcriptome mapping and profiling, as well as ChIP-Seq. Availability: Executables, source code, and sample data are available at http://socs.biology.gatech.edu/ Contact: nickbergman@gatech.edu Supplementary information: Supplementary data are available at Bioinformatics Online.
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spelling pubmed-26392732009-02-25 Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications Ondov, Brian D. Varadarajan, Anjana Passalacqua, Karla D. Bergman, Nicholas H. Bioinformatics Applications Note Summary: Here, we report the development of SOCS (short oligonucleotide color space), a program designed for efficient and flexible mapping of Applied Biosystems SOLiD sequence data onto a reference genome. SOCS performs its mapping within the context of ‘color space’, and it maximizes usable data by allowing a user-specified number of mismatches. Sequence census functions facilitate a variety of functional genomics applications, including transcriptome mapping and profiling, as well as ChIP-Seq. Availability: Executables, source code, and sample data are available at http://socs.biology.gatech.edu/ Contact: nickbergman@gatech.edu Supplementary information: Supplementary data are available at Bioinformatics Online. Oxford University Press 2008-12-01 2008-10-07 /pmc/articles/PMC2639273/ /pubmed/18842598 http://dx.doi.org/10.1093/bioinformatics/btn512 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Ondov, Brian D.
Varadarajan, Anjana
Passalacqua, Karla D.
Bergman, Nicholas H.
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
title Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
title_full Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
title_fullStr Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
title_full_unstemmed Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
title_short Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
title_sort efficient mapping of applied biosystems solid sequence data to a reference genome for functional genomic applications
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639273/
https://www.ncbi.nlm.nih.gov/pubmed/18842598
http://dx.doi.org/10.1093/bioinformatics/btn512
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