Genomes and knowledge - a questionable relationship?

被引:23
作者
Whitworth, David E. [1 ]
机构
[1] Aberystwyth Univ, Inst Biol Environm & Rural Sci, Aberystwyth SY23 3DD, Dyfed, Wales
关键词
D O I
10.1016/j.tim.2008.08.001
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The availability of bacterial genome sequences has ushered in an era of post-genomic research - accelerating and often enabling molecular genetic analyses. For bacteriologists focussing on an individual bacterium, comparing genomes has also led to a greater understanding of their favoured organism through contextualization. But how does the value of such contextualization vary with the number of available genomes? It seems that for most genome metrics, comparison against approximately 100 genomes is sufficient, with comparison against further genomes not considerably affecting the contextual knowledge gained. It appears that quality, rather than quantity, might be the most important factor when comparing genomes.
引用
收藏
页码:512 / 519
页数:8
相关论文
共 41 条
[31]   Complete genome sequence of the myxobacterium Sorangium cellulosum [J].
Schneiker, Susanne ;
Perlova, Olena ;
Kaiser, Olaf ;
Gerth, Klaus ;
Alici, Aysel ;
Altmeyer, Matthias O. ;
Bartels, Daniela ;
Bekel, Thomas ;
Beyer, Stefan ;
Bode, Edna ;
Bode, Helge B. ;
Bolten, Christoph J. ;
Choudhuri, Jomuna V. ;
Doss, Sabrina ;
Elnakady, Yasser A. ;
Frank, Bettina ;
Gaigalat, Lars ;
Goesmann, Alexander ;
Groeger, Carolin ;
Gross, Frank ;
Jelsbak, Lars ;
Jelsbak, Lotte ;
Kalinowski, Joern ;
Kegler, Carsten ;
Knauber, Tina ;
Konietzny, Sebastian ;
Kopp, Maren ;
Krause, Lutz ;
Krug, Daniel ;
Linke, Bukhard ;
Mahmud, Taifo ;
Martinez-Arias, Rosa ;
McHardy, Alice C. ;
Merai, Michelle ;
Meyer, Folker ;
Mormann, Sascha ;
Munoz-Dorado, Jose ;
Perez, Juana ;
Pradella, Silke ;
Rachid, Shwan ;
Raddatz, Guenter ;
Rosenau, Frank ;
Rueckert, Christian ;
Sasse, Florenz ;
Scharfe, Maren ;
Schuster, Stephan C. ;
Suen, Garret ;
Treuner-Lange, Anke ;
Velicer, Gregory J. ;
Vorhoelter, Frank-Joerg .
NATURE BIOTECHNOLOGY, 2007, 25 (11) :1281-1289
[32]   Structural biology sheds light on the puzzle genomic ORFans [J].
Siew, N ;
Fischer, D .
JOURNAL OF MOLECULAR BIOLOGY, 2004, 342 (02) :369-373
[33]   The COG database: a tool for genome-scale analysis of protein functions and evolution [J].
Tatusov, RL ;
Galperin, MY ;
Natale, DA ;
Koonin, EV .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :33-36
[34]   The Mosaic Genome of Anaeromyxobacter dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta- Proteobacteria [J].
Thomas, Sara H. ;
Wagner, Ryan D. ;
Arakaki, Adrian K. ;
Skolnick, Jeffrey ;
Kirby, John R. ;
Shimkets, Lawrence J. ;
Sanford, Robert A. ;
Loeffler, Frank E. .
PLOS ONE, 2008, 3 (05)
[35]   The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools [J].
Thompson, JD ;
Gibson, TJ ;
Plewniak, F ;
Jeanmougin, F ;
Higgins, DG .
NUCLEIC ACIDS RESEARCH, 1997, 25 (24) :4876-4882
[36]   Analysis for free: Comparing programs for sequence analysis [J].
Tippmann, HF .
BRIEFINGS IN BIOINFORMATICS, 2004, 5 (01) :82-87
[37]   Comparative genomic analysis of T-box regulatory systems in bacteria [J].
Vitreschak, Alexey G. ;
Mironov, Andrei A. ;
Lyubetsky, Vassily A. ;
Gelfand, Mikhail S. .
RNA, 2008, 14 (04) :717-735
[38]   Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization [J].
Wade, Joseph T. ;
Struhl, Kevin ;
Busby, Stephen J. W. ;
Grainger, David C. .
MOLECULAR MICROBIOLOGY, 2007, 65 (01) :21-26
[39]   Two-component systems of the myxobacteria: structure, diversity and evolutionary relationships [J].
Whitworth, David E. ;
Cock, Peter J. A. .
MICROBIOLOGY-SGM, 2008, 154 :360-372
[40]   Large-Scale Comparative Genomic Ranking of Taxonomically Restricted Genes (TRGs) in Bacterial and Archaeal Genomes [J].
Wilson, Gareth A. ;
Feil, Edward J. ;
Lilley, Andrew K. ;
Field, Dawn .
PLOS ONE, 2007, 2 (03)