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NAR
2000
120views more  NAR 2000»
10 years 11 months ago
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction
The WIT (What Is There) (http://wit.mcs.anl.gov/WIT2/ ) system has been designed to support comparative analysis of sequenced genomes and to generate metabolic reconstructions bas...
Ross A. Overbeek, Niels Larsen, Gordon D. Pusch, M...
CANDC
2004
ACM
10 years 11 months ago
Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea
We have addressed the distribution and abundance of 75 transcription factor (TF) families in complete genomes from 90 different bacterial and archaeal species. We found that the p...
Ernesto Pérez-Rueda, Julio Collado-Vides, L...
BMCBI
2004
115views more  BMCBI 2004»
10 years 11 months ago
An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage
Background: Eukaryotic whole genome sequences are accumulating at an impressive rate. Effective methods for comparing multiple whole eukaryotic genomes on a large scale are needed...
Gary W. Stuart, Michael W. Berry
BMCBI
2004
150views more  BMCBI 2004»
10 years 11 months ago
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
Background: The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity. It is important to quanti...
Saurabh Sinha, Mark D. Schroeder, Ulrich Unnerstal...
BMCBI
2004
86views more  BMCBI 2004»
10 years 11 months ago
A computer simulation analysis of the accuracy of partial genome sequencing and restriction fragment analysis in estimating gene
Background: Determination of genetic relatedness among microorganisms provides information necessary for making inferences regarding phylogeny. However, there is little informatio...
Baozhen Qiao, Ronald M. Weigel
BMCBI
2004
166views more  BMCBI 2004»
10 years 11 months ago
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models
Background: Many current gene prediction methods use only one model to represent proteincoding regions in a genome, and so are less likely to predict the location of genes that ha...
Shaun Mahony, James O. McInerney, Terry J. Smith, ...
BMCBI
2004
96views more  BMCBI 2004»
10 years 11 months ago
GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes
Background: An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes,...
Srikanth Celamkoti, Sashidhara Kundeti, Anjan Purk...
BMCBI
2004
154views more  BMCBI 2004»
10 years 11 months ago
Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments
Background: With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than ...
Ryan Brodie, Alex J. Smith, Rachel L. Roper, Vasil...
BMCBI
2005
115views more  BMCBI 2005»
10 years 11 months ago
MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays
Background: Enhancements in sequencing technology have recently yielded assemblies of large genomes including rat, mouse, human, fruit fly, and zebrafish. The availability of larg...
Eric C. Rouchka, Abdelnaby Khalyfa, Nigel G. F. Co...
BMCBI
2005
198views more  BMCBI 2005»
10 years 11 months ago
Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural
Background: The sequencing of the human genome has enabled us to access a comprehensive list of genes (both experimental and predicted) for further analysis. While a majority of t...
Qicheng Ma, Gung-Wei Chirn, Richard Cai, Joseph D....
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