An environmental signature for 323 microbial genomes based on codon adaptation indices
-
* Corresponding author: David W Ussery Dave@cbs.dtu.dk
Genome Biology 2006, 7:R114 doi:10.1186/gb-2006-7-12-r114
Accesses
- Last 30 days: 41 accesses
- Last 365 days: 378 accesses
- All time: 4269 accesses
Cited by
BioMed Central: 7 citations
|
Research
Humberto Peralta, Gabriela Guerrero, Alejandro Aguilar, Jaime Mora Biology Direct 2011, 6:48 (4 October 2011) Diversification of orthologous genes provokes specific physico-chemical changes in proteins of related species, revealing particular trends required to perform their functional roles in the adaptation to niche and intra-cellular conditions.
|
|
Research article
Analysis of intra-genomic GC content homogeneity within prokaryotes Jon Bohlin, Lars Snipen, Simon P Hardy, Anja B Kristoffersen, Karin Lagesen, Torunn Dønsvik, Eystein Skjerve, David W Ussery BMC Genomics 2010, 11:464 (6 August 2010) |
|
Research article
Jon Bohlin, Eystein Skjerve, David W Ussery BMC Genomics 2009, 10:487 (21 October 2009) |
|
Research
Community-wide analysis of microbial genome sequence signatures Gregory J Dick, Anders F Andersson, Brett J Baker, Sheri L Simmons, Brian C Thomas, A Pepper Yelton, Jillian F Banfield Genome Biology 2009, 10:R85 (21 August 2009) Genome signatures are used to identify and cluster sequences de novo from an acid biofilm microbial community metagenomic dataset, revealing information about the low-abundance community members. |
|
Research
CAIcal: A combined set of tools to assess codon usage adaptation Pere Puigbò, Ignacio G Bravo, Santiago Garcia-Vallve Biology Direct 2008, 3:38 (16 September 2008) The analysis of codon usage has been widely used for estimation of gene expressivity or gene adaptation, and may also be helpful for refining genome annotation.
|
|
Software
E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI) Pere Puigbò, Ignacio G Bravo, Santiago Garcia-Vallvé BMC Bioinformatics 2008, 9:65 (29 January 2008) |
|
Research article
Prediction of highly expressed genes in microbes based on chromatin accessibility Hanni Willenbrock, David W Ussery BMC Molecular Biology 2007, 8:11 (13 February 2007) Bacterial genes are highly expressed if their DNA structure tends to exclude chromatin, an association that is much better at predicting expression levels than codon usage perhaps because the DNA is accessible to transcriptional machinery.
|