RWN drafted portions of the manuscript and performed alignments and comparative genomic analysis of the short read data.
PileUp and Pretty programs of the Wisconsin Package, Version 10 (Genetic Computer Group, 2000, Madison, WI), were used to produce sequence alignments and comparative nucleotide analyses.
DF participated to the project design, designed the primers, assembled the BAC contigs based on EST anchoring, did the sequence alignment and the comparative maps, and drafted the manuscript.
As an example, Table 2 shows the results of both the sequence alignment and a comparative hybridization analyzed with TAS and our JAVA tool for the gene clusters containing wbp and related genes that are involved in the synthesis of lipopolysaccharides (LPS).
The alignments and the comparative pipeline described here were adopted by the Mouse Encode Consortium for the cross-species mapping of TFos.
The community stands in urgent expectation of a solution to this bioinformatics dilemma for robust genome assemblies, for gene and genome feature annotations, for genome alignments, and for comparative analyses.
To identify the complete set of conserved, novel, and expanded potassium channel and potassium channel-related genes (K-Channels) in the zebra finch genome we used a comprehensive strategy consisting of mRNA/protein alignments, syntenic analysis, and comparative genomics.
After direct sequencing and comparative alignment with GenBank sequences, identical R. rickettsii ompA sequences were obtained from the patient's blood and the tick (Table).
Based on codon usage and comparative alignment with sequences from other Plasmodium species, these heptads are best explained by a recent tandem duplication of a single heptad motif in P. falciparum or its immediate ancestor [ 31].
