[1]杨一子,罗大民.向HelmCoP数据库直系同源组添加古菌序列[J].南京师大学报(自然科学版),2014,37(03):89.
　Yang Yizi,Luo Damin.Assigning Archaeal Sequences to HelmCoP Groups[J].Journal of Nanjing Normal University(Natural Science Edition),2014,37(03):89.
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向HelmCoP数据库直系同源组添加古菌序列()
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《南京师大学报（自然科学版）》[ISSN:1001-4616/CN:32-1239/N]

卷:
第37卷
期数:
2014年03期
页码:
89
栏目:
生命科学
出版日期:
2014-09-30

文章信息/Info

Title:
Assigning Archaeal Sequences to HelmCoP Groups
作者:
杨一子1; 罗大民1; 2
(1.厦门大学生命科学学院,福建 厦门,361005)(2.厦门大学细胞应激生物学国家重点实验室,福建 厦门,361005)
Author(s):
Yang Yizi1; Luo Damin1; 2
(1.School of Life Sciences,Xiamen University,Xiamen 361005,China)(2.State Key Laboratory of Cellular Stress Biology,Xiamen University,Xiamen 361005,China)
关键词:
古菌; OrthoMCL; HelmCoP; BLAST
Keywords:
Archaea; OrthoMCL; HelmCoP; BLAST
分类号:
TP311.13
文献标志码:
A
摘要:
含有古菌序列的直系同源组可以在很大程度上便利各种基于HelmCoP数据的研究,但是目前HelmCoP直系同源组不含有任何古菌序列.为了向HelmCoP直系同源组添加古菌序列,以1个OrthoMCL-DB网站工具的分配方法为依据,我们将29种古菌物种模式菌株的蛋白质组数据,通过BLAST比对和OrthoMCL分析,逐步添加至各个HelmCoP直系同源组中.结果显示,21 326条古菌序列被成功地分配给了1 954个HelmCoP直系同源组中,而其他2 821条古菌序列被归类至NO_GROUP类别.这些分配结果得到了良好BLAST匹配数据的支持.一些自由生活物种包括Caenorhabditis japonica、大豆和拟南芥在研究中也受到了关注,因为这些物种相当多的基因在古菌物种内有同源基因.
Abstract:
Orthologous groups containing archaeal sequences could facilitate many researches based on HelmCoP data,but unfortunately there were no archaeal sequences in HelmCoP groups.To assign archaeal sequences to HelmCoP groups,we assigned sequences in proteomes of 29 type strains of multiple archaeal species to HelmCoP groups through both BLAST search and OrthoMCL analysis,according to the protocol for assigning sequences by a OrthoMCL-DB web tool.The results showed that 21 326 archaeal sequences were successfully assigned to 1 954 HelmCoP groups,and other 2 821 sequences were assigned to NO_GROUP.These assignments gained support from quite good BLAST hits.In addition,some free-living species including Caenorhabditis japonica,soybean,and thale cress were also highlighted in this study,because many genes of these species had homologs in archaeal species.

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备注/Memo

备注/Memo:
收稿日期:2014-03-16.
基金项目:国家自然科学基金(81171595)、福建省自然科学基金(2010J01229).
通讯联系人:罗大民,教授,博导,研究方向:寄生虫学.E-mail:dmluo@xmu.edu.cn
更新日期/Last Update: 2014-09-30