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
[1]   Informatics for unveiling hidden genome signatures [J].
Abe, T ;
Kanaya, S ;
Kinouchi, M ;
Ichiba, Y ;
Kozuki, T ;
Ikemura, T .
GENOME RESEARCH, 2003, 13 (04) :693-702
[2]   Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori [J].
Alm, RA ;
Ling, LSL ;
Moir, DT ;
King, BL ;
Brown, ED ;
Doig, PC ;
Smith, DR ;
Noonan, B ;
Guild, BC ;
deJonge, BL ;
Carmel, G ;
Tummino, PJ ;
Caruso, A ;
Uria-Nickelsen, M ;
Mills, DM ;
Ives, C ;
Gibson, R ;
Merberg, D ;
Mills, SD ;
Jiang, Q ;
Taylor, DE ;
Vovis, GF ;
Trost, TJ .
NATURE, 1999, 397 (6715) :176-180
[3]  
Ashburner M, 2001, GENOME RES, V11, P1425
[4]  
Baba Tomoya, 2008, V416, P183, DOI 10.1007/978-1-59745-321-9_12
[5]   Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration [J].
Bauer, Sebastian ;
Grossmann, Steffen ;
Vingron, Martin ;
Robinson, Peter N. .
BIOINFORMATICS, 2008, 24 (14) :1650-1651
[6]   Making informed decisions: regulatory interactions between two-component systems [J].
Bijisma, JJE ;
Groisman, EA .
TRENDS IN MICROBIOLOGY, 2003, 11 (08) :359-366
[7]   Functional classification using phylogenomic inference [J].
Brown, Duncan ;
Sjolander, Kimmen .
PLOS COMPUTATIONAL BIOLOGY, 2006, 2 (06) :479-483
[8]   Genome sequence of lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion [J].
Callanan, Michael ;
Kaleta, Pawel ;
O'Callaghan, John ;
O'Sullivan, Orla ;
Jordan, Kieran ;
McAuliffe, Olivia ;
Sangrador-Vegas, Amaia ;
Slattery, Lydia ;
Fitzgerald, Gerald F. ;
Beresford, Tom ;
Ross, R. Paul .
JOURNAL OF BACTERIOLOGY, 2008, 190 (02) :727-735
[9]   Evolution of gene overlaps: Relative reading frame bias in prokaryotic two-component system genes [J].
Cock, Peter J. A. ;
Whitworth, David E. .
JOURNAL OF MOLECULAR EVOLUTION, 2007, 64 (04) :457-462
[10]   Evolution of prokaryotic two-component system signaling pathways: Gene fusions and fissions [J].
Cock, Peter J. A. ;
Whitworth, David E. .
MOLECULAR BIOLOGY AND EVOLUTION, 2007, 24 (11) :2355-2357