A Review of Recent Alignment-Free Clustering Algorithms in Expressed Sequence Tag
Expressed sequence tags (ESTs) are short single pass sequence reads derived from cDNA libraries, they have been used for gene discovery, detection of splice variants, expression of genes and also transciptome analysis. Clustering of ESTs is a vital step before they can be processed further. Currentl...
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| Format: | Conference or Workshop Item |
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2009
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| Online Access: | http://shdl.mmu.edu.my/1930/ |
| _version_ | 1848789916988735488 |
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| author | Ng, Keng-Hoong Phon-Amnuaisuk, Somnuk Ho, Chin-Kuan |
| author_facet | Ng, Keng-Hoong Phon-Amnuaisuk, Somnuk Ho, Chin-Kuan |
| author_sort | Ng, Keng-Hoong |
| building | MMU Institutional Repository |
| collection | Online Access |
| description | Expressed sequence tags (ESTs) are short single pass sequence reads derived from cDNA libraries, they have been used for gene discovery, detection of splice variants, expression of genes and also transciptome analysis. Clustering of ESTs is a vital step before they can be processed further. Currently there are many EST clustering algorithms available. Basically they can be generalized into two broad approaches, i.e. alignment-based and alignment-free. The former approach is reliable but inefficient in terms of running time, while the latter approach is gaining popularity and currently under rapid development due to its faster speed and acceptable result. In this paper, we propose a taxonomy for sequence comparison algorithms and another taxonomy for EST clustering algorithms. In addition, we also highlight the peculiarities of recently introduced alignment-free EST clustering algorithms by focusing on their features, distance measures, advantages and disadvantages. |
| first_indexed | 2025-11-14T18:04:20Z |
| format | Conference or Workshop Item |
| id | mmu-1930 |
| institution | Multimedia University |
| institution_category | Local University |
| last_indexed | 2025-11-14T18:04:20Z |
| publishDate | 2009 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | mmu-19302011-09-23T03:21:47Z http://shdl.mmu.edu.my/1930/ A Review of Recent Alignment-Free Clustering Algorithms in Expressed Sequence Tag Ng, Keng-Hoong Phon-Amnuaisuk, Somnuk Ho, Chin-Kuan T Technology (General) QA75.5-76.95 Electronic computers. Computer science Expressed sequence tags (ESTs) are short single pass sequence reads derived from cDNA libraries, they have been used for gene discovery, detection of splice variants, expression of genes and also transciptome analysis. Clustering of ESTs is a vital step before they can be processed further. Currently there are many EST clustering algorithms available. Basically they can be generalized into two broad approaches, i.e. alignment-based and alignment-free. The former approach is reliable but inefficient in terms of running time, while the latter approach is gaining popularity and currently under rapid development due to its faster speed and acceptable result. In this paper, we propose a taxonomy for sequence comparison algorithms and another taxonomy for EST clustering algorithms. In addition, we also highlight the peculiarities of recently introduced alignment-free EST clustering algorithms by focusing on their features, distance measures, advantages and disadvantages. 2009-12 Conference or Workshop Item NonPeerReviewed Ng, Keng-Hoong and Phon-Amnuaisuk, Somnuk and Ho, Chin-Kuan (2009) A Review of Recent Alignment-Free Clustering Algorithms in Expressed Sequence Tag. In: International Conference of Soft Computing and Pattern Recognition, DEC 04-07, 2009 , Malacca, MALAYSIA. http://dx.doi.org/10.1109/SoCPaR.2009.18 doi:10.1109/SoCPaR.2009.18 doi:10.1109/SoCPaR.2009.18 |
| spellingShingle | T Technology (General) QA75.5-76.95 Electronic computers. Computer science Ng, Keng-Hoong Phon-Amnuaisuk, Somnuk Ho, Chin-Kuan A Review of Recent Alignment-Free Clustering Algorithms in Expressed Sequence Tag |
| title | A Review of Recent Alignment-Free Clustering Algorithms in Expressed Sequence Tag |
| title_full | A Review of Recent Alignment-Free Clustering Algorithms in Expressed Sequence Tag |
| title_fullStr | A Review of Recent Alignment-Free Clustering Algorithms in Expressed Sequence Tag |
| title_full_unstemmed | A Review of Recent Alignment-Free Clustering Algorithms in Expressed Sequence Tag |
| title_short | A Review of Recent Alignment-Free Clustering Algorithms in Expressed Sequence Tag |
| title_sort | review of recent alignment-free clustering algorithms in expressed sequence tag |
| topic | T Technology (General) QA75.5-76.95 Electronic computers. Computer science |
| url | http://shdl.mmu.edu.my/1930/ http://shdl.mmu.edu.my/1930/ http://shdl.mmu.edu.my/1930/ |