Comparative Genomics via Wavelet Analysis for Closely Related Bacteria
<p/> <p>Comparative genomics has been a valuable method for extracting and extrapolating genome information among closely related bacteria. The efficiency of the traditional methods is extremely influenced by the software method used. To overcome the problem here, we propose using wavele...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
SpringerOpen
2004-01-01
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| Series: | EURASIP Journal on Advances in Signal Processing |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1155/S1110865704309170 |
| _version_ | 1819160443647688704 |
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| author | Song Jiuzhou Ware Tony Liu Shu-Lin Surette M |
| author_facet | Song Jiuzhou Ware Tony Liu Shu-Lin Surette M |
| author_sort | Song Jiuzhou |
| collection | DOAJ |
| description | <p/> <p>Comparative genomics has been a valuable method for extracting and extrapolating genome information among closely related bacteria. The efficiency of the traditional methods is extremely influenced by the software method used. To overcome the problem here, we propose using wavelet analysis to perform comparative genomics. First, global comparison using wavelet analysis gives the difference at a quantitative level. Then local comparison using keto-excess or purine-excess plots shows precise positions of inversions, translocations, and horizontally transferred DNA fragments. We firstly found that the level of energy spectra difference is related to the similarity of bacteria strains; it could be a quantitative index to describe the similarities of genomes. The strategy is described in detail by comparisons of closely related strains: <it>S.typhi</it> CT18, <it>S.typhi</it> Ty2, <it>S.typhimurium</it> LT2, <it>H.pylori</it> 26695, and <it>H.pylori</it> J99.</p> |
| first_indexed | 2024-12-22T16:56:32Z |
| format | Article |
| id | doaj.art-57e3eda53ec347a7856ea103cdfc6ba7 |
| institution | Directory Open Access Journal |
| issn | 1687-6172 1687-6180 |
| language | English |
| last_indexed | 2024-12-22T16:56:32Z |
| publishDate | 2004-01-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | EURASIP Journal on Advances in Signal Processing |
| spelling | doaj.art-57e3eda53ec347a7856ea103cdfc6ba72022-12-21T18:19:26ZengSpringerOpenEURASIP Journal on Advances in Signal Processing1687-61721687-61802004-01-0120041890421Comparative Genomics via Wavelet Analysis for Closely Related BacteriaSong JiuzhouWare TonyLiu Shu-LinSurette M<p/> <p>Comparative genomics has been a valuable method for extracting and extrapolating genome information among closely related bacteria. The efficiency of the traditional methods is extremely influenced by the software method used. To overcome the problem here, we propose using wavelet analysis to perform comparative genomics. First, global comparison using wavelet analysis gives the difference at a quantitative level. Then local comparison using keto-excess or purine-excess plots shows precise positions of inversions, translocations, and horizontally transferred DNA fragments. We firstly found that the level of energy spectra difference is related to the similarity of bacteria strains; it could be a quantitative index to describe the similarities of genomes. The strategy is described in detail by comparisons of closely related strains: <it>S.typhi</it> CT18, <it>S.typhi</it> Ty2, <it>S.typhimurium</it> LT2, <it>H.pylori</it> 26695, and <it>H.pylori</it> J99.</p>http://dx.doi.org/10.1155/S1110865704309170comparative genomicsgene discoverywavelet analysisbacterial genome |
| spellingShingle | Song Jiuzhou Ware Tony Liu Shu-Lin Surette M Comparative Genomics via Wavelet Analysis for Closely Related Bacteria EURASIP Journal on Advances in Signal Processing comparative genomics gene discovery wavelet analysis bacterial genome |
| title | Comparative Genomics via Wavelet Analysis for Closely Related Bacteria |
| title_full | Comparative Genomics via Wavelet Analysis for Closely Related Bacteria |
| title_fullStr | Comparative Genomics via Wavelet Analysis for Closely Related Bacteria |
| title_full_unstemmed | Comparative Genomics via Wavelet Analysis for Closely Related Bacteria |
| title_short | Comparative Genomics via Wavelet Analysis for Closely Related Bacteria |
| title_sort | comparative genomics via wavelet analysis for closely related bacteria |
| topic | comparative genomics gene discovery wavelet analysis bacterial genome |
| url | http://dx.doi.org/10.1155/S1110865704309170 |
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