Comparative genomic workflow
his article describes a workflow for identifying conserved patterns in noncoding regions of vertebrate genomes, with an intention of investigating possible functions of the conserved regions. The annotations of genomes are collected from the Ensembl database. The sequences are then arranged to use f...
| Main Authors: | , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Institute of Electrical and Electronics Engineers
2010
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| Online Access: | http://hdl.handle.net/1721.1/60264 |
| _version_ | 1826188321688125440 |
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| author | Rajapakse, Jagath Pooja Chen, Chunxi Ho, Sy-Loi |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Rajapakse, Jagath Pooja Chen, Chunxi Ho, Sy-Loi |
| author_sort | Rajapakse, Jagath |
| collection | MIT |
| description | his article describes a workflow for identifying conserved patterns in noncoding regions of vertebrate genomes, with an intention of investigating possible functions of the conserved regions. The annotations of genomes are collected from the Ensembl database. The sequences are then arranged to use for sequence alignment with basic local alignment search tool Z (BLASTZ) [10], which finds gap- free alignments of at least q% identity and I b/s in length. All the conserved noncoding regions identified are stored in a relational database. An user-friendly Web interface provides easy access to conserved regions and related information and visualization capabilities. |
| first_indexed | 2024-09-23T07:57:53Z |
| format | Article |
| id | mit-1721.1/60264 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T07:57:53Z |
| publishDate | 2010 |
| publisher | Institute of Electrical and Electronics Engineers |
| record_format | dspace |
| spelling | mit-1721.1/602642022-09-30T01:18:09Z Comparative genomic workflow Rajapakse, Jagath Pooja Chen, Chunxi Ho, Sy-Loi Massachusetts Institute of Technology. Department of Biological Engineering Rajapakse, Jagath C Rajapakse, Jagath his article describes a workflow for identifying conserved patterns in noncoding regions of vertebrate genomes, with an intention of investigating possible functions of the conserved regions. The annotations of genomes are collected from the Ensembl database. The sequences are then arranged to use for sequence alignment with basic local alignment search tool Z (BLASTZ) [10], which finds gap- free alignments of at least q% identity and I b/s in length. All the conserved noncoding regions identified are stored in a relational database. An user-friendly Web interface provides easy access to conserved regions and related information and visualization capabilities. Singapore. Biomedical Research Council (grant no. 04/1/22/19/376) National Grid (Singapore) Sun Microsystems 2010-12-10T19:02:41Z 2010-12-10T19:02:41Z 2009-07 2009-07 Article http://purl.org/eprint/type/JournalArticle 0739-5175 INSPEC Accession Number: 10781332 http://hdl.handle.net/1721.1/60264 Rajapakse, J. et al. “Comparative genomic workflow.” Engineering in Medicine and Biology Magazine, IEEE 28.4 (2009): 19-24. ©2009 IEEE. PubMed ID: 19622420 en_US http://dx.doi.org/10.1109/MEMB.2009.932910 IEEE Engineering in Medicine and Biology Magazine Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf Institute of Electrical and Electronics Engineers IEEE |
| spellingShingle | Rajapakse, Jagath Pooja Chen, Chunxi Ho, Sy-Loi Comparative genomic workflow |
| title | Comparative genomic workflow |
| title_full | Comparative genomic workflow |
| title_fullStr | Comparative genomic workflow |
| title_full_unstemmed | Comparative genomic workflow |
| title_short | Comparative genomic workflow |
| title_sort | comparative genomic workflow |
| url | http://hdl.handle.net/1721.1/60264 |
| work_keys_str_mv | AT rajapaksejagath comparativegenomicworkflow AT pooja comparativegenomicworkflow AT chenchunxi comparativegenomicworkflow AT hosyloi comparativegenomicworkflow |