|Table of Contents|

Assigning Archaeal Sequences to HelmCoP Groups(PDF)

《南京师大学报（自然科学版）》[ISSN:1001-4616/CN:32-1239/N]

Issue:
2014年03期
Page:
89-
Research Field:
生命科学
Publishing date:

Info

Title:
Assigning Archaeal Sequences to HelmCoP Groups
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)
Keywords:
Archaea; OrthoMCL; HelmCoP; BLAST
PACS:
TP311.13
DOI:
-
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.

References:

[1] Brinkmann H,Philippe H.Archaea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies[J].Molecular Biology and Evolution,1999,16(6):817-825.
[2]Baldauf S L.The deep roots of eukaryotes[J].Science,2003,300(5626):1 703-1 706.
[3]Derelle R,Lang B F.Rooting the eukaryotic tree with mitochondrial and bacterial proteins[J].Molecular Biology and Evolution,2012,29(4):1 277-1 289.
[4]Brown J R.Ancient horizontal gene transfer[J].Nature Review Genetics,2003,4(2):121-132.
[5]Abubucker S,Martin J,Taylor C M,et al.HelmCoP:an online resource for helminth functional genomics and drug and vaccine targets prioritization[J].PloS One,2011,6(7):e21832.
[6]Fischer S,Brunk B P,Chen F,et al.Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups[J].Current Protocols in Bioinformatics,2011,6:1-19.
[7]Chen F,Mackey A J,Stoeckert C J,et al.OrthoMCL-DB:querying a comprehensive multi-species collection of ortholog groups[J].Nucleic Acids Research,2006,34(Suppl 1):D363-D368.
[8]Altschul S F,Gish W,Miller W,et al.Basic local alignment search tool[J].Journal of Molecular Biology,1990,215(3):403-410.
[9]Li L,Stoeckert C J Jr,Roos D S.OrthoMCL:identification of ortholog groups for eukaryotic genomes[J].Genome Research,2003,13(9):2 178-2 189.
[10]Kersey P J,Staines D M,Lawson D,et al.Ensembl Genomes:an integrative resource for genome-scale data from non-vertebrate species[J].Nucleic Acids Research,2012,40(D1):D91-D97.
[11]Franzmann P D,Liu Y,Balkwill D L,et al.Methanogenium frigidum sp.nov.,a psychrophilic,H2-using methanogen from Ace Lake,Antarctica[J].International Journal of Systematic Bacteriology,1997,47(4):1 068-1 072.
[12]Gribaldo S,Brochier-Armanet C.The origin and evolution of Archaea:a state of the art[J].Philosophical Transactions of the Royal Society of London Series B Biological Sciences,2006,361(1470):1 007-1 022.
[13]Alsmark C,Foster P G,Sicheritz-Ponten T,et al.Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes[J].Genome Biology,2013,25,14(2):R19.
[14]Camacho C,Coulouris G,Avagyan V,et al.BLAST+:architecture and applications[J].BMC Bioinformatics,2009,10(1):421.
[15]Okumura E,Ishikawa Y,Tanaka R,et al.Propagation of Caenorhabditis japonica in the nest of its carrier insect,Parastrachia japonensis[J].Zoological Science,2013,30(3):174-177.
[16]Kiontke K,Sudhaus W.Ecology of Caenorhabditis species[J].WormBook,2006:1-14.
[17]Nongbri P L,Vahabi K,Mrozinska A,et al.Balancing defense and growth—Analyses of the beneficial symbiosis between Piriformospora indica and Arabidopsis thaliana[J].Symbiosis,2013,58(1/3):17-28.

Memo

Memo:
-
Last Update: 2014-09-30