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Host-parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity
https://sucra.repo.nii.ac.jp/records/13394
https://sucra.repo.nii.ac.jp/records/13394fcdf4789-4d3c-4b51-81a8-6e6448ccd191
名前 / ファイル | ライセンス | アクション |
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A1002844.pdf (448.2 kB)
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Item type | 学術雑誌論文 / Journal Article(1) | |||||
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公開日 | 2009-05-11 | |||||
タイトル | ||||||
タイトル | Host-parasite relations of bacteria and phages can be unveiled by Oligostickiness, a measure of relaxed sequence similarity | |||||
言語 | ||||||
言語 | eng | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
資源タイプ | journal article | |||||
著者 |
Ahmed, Shamim
× Ahmed, Shamim× Saito, Ayumu× Suzuki, Miho× Nemoto, Naoto× 西垣, 功一 |
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著者 ローマ字 | ||||||
Ahmed, Shamim | ||||||
著者 ローマ字 | ||||||
Saito, Ayumu | ||||||
著者 ローマ字 | ||||||
Suzuki, Miho | ||||||
著者 ローマ字 | ||||||
Nemoto, Naoto | ||||||
著者 ローマ字 | ||||||
Nishigaki, Koichi | ||||||
著者 所属 | ||||||
著者 所属 | ||||||
著者 所属 | ||||||
著者 所属 | ||||||
著者 所属 | ||||||
埼玉大学大学院理工学研究科物質科学部門 | ||||||
著者 所属(別言語) | ||||||
著者 所属(別言語) | ||||||
著者 所属(別言語) | ||||||
著者 所属(別言語) | ||||||
著者 所属(別言語) | ||||||
Graduate School of Science and Engineering, Saitama University | ||||||
書誌情報 |
BIOINFORMATICS 巻 25, 号 5, p. 563-570, 発行日 2009 |
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年月次 | ||||||
2009-3 | ||||||
出版者名 | ||||||
出版者 | Oxford University Press | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 13674803 | |||||
DOI | ||||||
関連タイプ | isVersionOf | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1093/bioinformatics/btp003 | |||||
関連サイト | ||||||
内容記述タイプ | Other | |||||
内容記述 | http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/5/563 | http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/5/563 | |||||
抄録 | ||||||
内容記述タイプ | Abstract | |||||
内容記述 | Motivation: The recent metagenome analysis has been producing a large number of host-unassigned viruses. Although assigning viruses to their hosts is basically important not only for virology but also for prevention of epidemic, it has been a laborious and difficult task to date. The only effective method for this purpose has been to find them in a same microscopic view. Now, we tried a computational approach based on genome sequences of bacteria and phages, introducing a physicochemical parameter, SOSS (set of oligostickiness similarity score) derived from oligostickiness, a measure of binding affinity of oligonucleotides to template DNA. Results: We could confirm host-parasite relationships of bacteria and their phages by SOSS analysis: all phages tested (25 species) had a remarkably higher SOSS value with its host than with unrelated bacteria. Interestingly, according to SOSS values, lysogenic phages such as lambda phage (host: Escherichia coli) or SPP1 (host: Bacillus subtilis) have distinctively higher similarity with its host than its non-lysogenic (excretive or virulent) ones such as fd and T4 (host: E. coli) or phages gamma and PZA (host: B. subtilis). This finding is very promising for assigning host-unknown viruses to its host. We also investigated the relationship in codon usage frequency or G+C content of genomes to interpret the phenomenon revealed by SOSS analysis, obtaining evidences which support the hypothesis that higher SOSS values resulted from the cohabitation in the same environment which may cause the common biased mutation. Thus, lysogenic phages which stay inside longer resemble the host. |
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版 | ||||||
[著者版] | ||||||
著者版フラグ | ||||||
出版タイプ | AM | |||||
出版タイプResource | http://purl.org/coar/version/c_ab4af688f83e57aa | |||||
資源タイプ | ||||||
内容記述タイプ | Other | |||||
内容記述 | text | |||||
フォーマット | ||||||
内容記述タイプ | Other | |||||
内容記述 | application/pdf | |||||
作成日 | ||||||
日付 | 2009-05-11 | |||||
日付タイプ | Created | |||||
アイテムID | ||||||
A1002844 |