메뉴 건너뛰기




Volumn 2016, Issue 1, 2016, Pages

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

Author keywords

Candidate phyla radiation; Complete genomes; Metagenomics; Peregrinibacteria; Strain variation

Indexed keywords

ACETYL COENZYME A; CYTOCHROME C OXIDASE; FLAVOPROTEIN; ISOPRENOID; MEVALONIC ACID; PEPTIDOGLYCAN; RHAMNOSE; RIBOSOME RNA; RNA 16S;

EID: 84957584565     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.1607     Document Type: Article
Times cited : (42)

References (29)
  • 3
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5):1792-1797 DOI 10.1093/nar/gkh340.
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 4
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460-2461 DOI 10.1093/bioinformatics/btq461.
    • (2010) Bioinformatics , vol.26 , Issue.19 , pp. 2460-2461
    • Edgar, R.C.1
  • 5
    • 85028258790 scopus 로고    scopus 로고
    • Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla
    • Epub ahead of print 8 April 2015
    • Emerson JB, Thomas BC, Alvarez W, Banfield JF. 2015. Metagenomic analysis of a high carbon dioxide subsurface microbial community populated by chemolithoautotrophs and bacteria and archaea from candidate phyla. Environmental Microbiology Epub ahead of print 8 April 2015 DOI 10.1111/1462-2920.12817.
    • (2015) Environmental Microbiology
    • Emerson, J.B.1    Thomas, B.C.2    Alvarez, W.3    Banfield, J.F.4
  • 6
    • 17444423723 scopus 로고    scopus 로고
    • Folate cross-feeding supports symbiotic homoacetogenic spirochetes
    • Graber JR, Breznak JA. 2005. Folate cross-feeding supports symbiotic homoacetogenic spirochetes. Applied and Environmental Microbiology 71(4):1883-1889 DOI 10.1128/AEM.71.4.1883-1889.2005.
    • (2005) Applied and Environmental Microbiology , vol.71 , Issue.4 , pp. 1883-1889
    • Graber, J.R.1    Breznak, J.A.2
  • 10
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S. 2000. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28(1):27-30 DOI 10.1093/nar/28.1.27.
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 13
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357-359 DOI 10.1038/nmeth.1923.
    • (2012) Nature Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 14
    • 78650467548 scopus 로고    scopus 로고
    • Origins and early evolution of the mevalonate pathway of isoprenoid biosynthesis in the three domains of life
    • Lombard J, Moreira D. 2010. Origins and early evolution of the mevalonate pathway of isoprenoid biosynthesis in the three domains of life. Molecular Biology and Evolution 28(1):87-99 DOI 10.1093/molbev/msq177.
    • (2010) Molecular Biology and Evolution , vol.28 , Issue.1 , pp. 87-99
    • Lombard, J.1    Moreira, D.2
  • 16
    • 0034973392 scopus 로고    scopus 로고
    • Sortase-catalysed anchoring of surface proteins to the cell wall of Staphylococcus aureus
    • Mazmanian SK, Ton-That H, Schneewind O. 2001. Sortase-catalysed anchoring of surface proteins to the cell wall of Staphylococcus aureus. Molecular Microbiology 40(5):1049-1057 DOI 10.1046/j.1365-2958.2001.02411.x.
    • (2001) Molecular Microbiology , vol.40 , Issue.5 , pp. 1049-1057
    • Mazmanian, S.K.1    Ton-That, H.2    Schneewind, O.3
  • 17
    • 84886383710 scopus 로고    scopus 로고
    • Relative amino acid composition signatures of organisms and environments
    • Moura A, Savageau MA, Alves R. 2013. Relative amino acid composition signatures of organisms and environments. PLoS ONE 8(10):e77319 DOI 10.1371/journal.pone.0077319.
    • (2013) PLoS ONE , vol.8 , Issue.10
    • Moura, A.1    Savageau, M.A.2    Alves, R.3
  • 18
    • 84870061381 scopus 로고    scopus 로고
    • Lipoproteins in bacteria: structures and biosynthetic pathways
    • Nakayama H, Kurokawa K, Lee BL. 2012. Lipoproteins in bacteria: structures and biosynthetic pathways. FEBS Journal 279(23):4247-4268 DOI 10.1111/febs.12041.
    • (2012) FEBS Journal , vol.279 , Issue.23 , pp. 4247-4268
    • Nakayama, H.1    Kurokawa, K.2    Lee, B.L.3
  • 20
    • 84861760530 scopus 로고    scopus 로고
    • IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
    • Peng Y, Leung HCM, Yiu SM, Chin FYL. 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28(11):1420-1428 DOI 10.1093/bioinformatics/bts174.
    • (2012) Bioinformatics , vol.28 , Issue.11 , pp. 1420-1428
    • Peng, Y.1    Leung, H.C.M.2    Yiu, S.M.3    Chin, F.Y.L.4
  • 21
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research 35(21):7188-7196 DOI 10.1093/nar/gkm864.
    • (2007) Nucleic Acids Research , vol.35 , Issue.21 , pp. 7188-7196
    • Pruesse, E.1    Quast, C.2    Knittel, K.3    Fuchs, B.M.4    Ludwig, W.5    Peplies, J.6    Glöckner, F.O.7
  • 22
    • 33847280283 scopus 로고    scopus 로고
    • Prediction of effective genome size in metagenomic samples
    • Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P. 2007. Prediction of effective genome size in metagenomic samples. Genome Biology 8(1):R10 DOI 10.1186/gb-2007-8-1-r10.
    • (2007) Genome Biology , vol.8 , Issue.1 , pp. R10
    • Raes, J.1    Korbel, J.O.2    Lercher, M.J.3    von Mering, C.4    Bork, P.5
  • 23
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312-1313 DOI 10.1093/bioinformatics/btu033.
    • (2014) Bioinformatics , vol.30 , Issue.9 , pp. 1312-1313
    • Stamatakis, A.1
  • 24
    • 34347388470 scopus 로고    scopus 로고
    • UniRef: comprehensive and non-redundant UniProt reference clusters
    • Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH. 2007. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23(10):1282-1288 DOI 10.1093/bioinformatics/btm098.
    • (2007) Bioinformatics , vol.23 , Issue.10 , pp. 1282-1288
    • Suzek, B.E.1    Huang, H.2    McGarvey, P.3    Mazumder, R.4    Wu, C.H.5
  • 25
    • 61849113253 scopus 로고    scopus 로고
    • Graph clustering via a discrete uncoupling process
    • Van Dongen S. 2008. Graph clustering via a discrete uncoupling process. SIAM Journal on Matrix Analysis and Applications 30(1):121-141 DOI 10.1137/040608635.
    • (2008) SIAM Journal on Matrix Analysis and Applications , vol.30 , Issue.1 , pp. 121-141
    • Van Dongen, S.1
  • 28
    • 77954199597 scopus 로고    scopus 로고
    • PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
    • Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FSL. 2010. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26(13):1608-1615 DOI 10.1093/bioinformatics/btq249.
    • (2010) Bioinformatics , vol.26 , Issue.13 , pp. 1608-1615
    • Yu, N.Y.1    Wagner, J.R.2    Laird, M.R.3    Melli, G.4    Rey, S.5    Lo, R.6    Dao, P.7    Sahinalp, S.C.8    Ester, M.9    Foster, L.J.10    Brinkman, F.S.L.11
  • 29
    • 77956967295 scopus 로고    scopus 로고
    • Using the velvet de novo assembler for short-read sequencing technologies
    • Chapter 11, Unit 11.5
    • Zerbino DR. 2010. Using the velvet de novo assembler for short-read sequencing technologies. Current Protocols in Bioinformatics. Chapter 11:Unit 11.5 DOI 10.1002/0471250953.bi1105s31.
    • (2010) Current Protocols in Bioinformatics
    • Zerbino, D.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.