FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology
Next-generation sequencing can provide insight into protein-DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We pres...
| Main Authors: | , , , , , |
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| Format: | Journal Article |
| Published: |
Oxford University Press
2008
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| Online Access: | http://hdl.handle.net/20.500.11937/4856 |
| _version_ | 1848744633818939392 |
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| author | Fejes, A. Robertson, G. Bilenky, M. Varhol, Richard Bainbridge, M. Jones, S. |
| author_facet | Fejes, A. Robertson, G. Bilenky, M. Varhol, Richard Bainbridge, M. Jones, S. |
| author_sort | Fejes, A. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Next-generation sequencing can provide insight into protein-DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom 'WIG' track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads. © 2008 The Author(s). |
| first_indexed | 2025-11-14T06:04:34Z |
| format | Journal Article |
| id | curtin-20.500.11937-4856 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T06:04:34Z |
| publishDate | 2008 |
| publisher | Oxford University Press |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-48562017-09-13T14:45:10Z FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology Fejes, A. Robertson, G. Bilenky, M. Varhol, Richard Bainbridge, M. Jones, S. Next-generation sequencing can provide insight into protein-DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom 'WIG' track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads. © 2008 The Author(s). 2008 Journal Article http://hdl.handle.net/20.500.11937/4856 10.1093/bioinformatics/btn305 Oxford University Press unknown |
| spellingShingle | Fejes, A. Robertson, G. Bilenky, M. Varhol, Richard Bainbridge, M. Jones, S. FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
| title | FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
| title_full | FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
| title_fullStr | FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
| title_full_unstemmed | FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
| title_short | FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
| title_sort | findpeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology |
| url | http://hdl.handle.net/20.500.11937/4856 |