Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

doi:10.1186/1471-2105-8-173

BMC Bioinformatics

Volume 8

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Research article

Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

Raja Jothi , Teresa M Przytycka and L Aravind

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

author email corresponding author email

BMC Bioinformatics 2007, 8:173doi:10.1186/1471-2105-8-173


Published:	23 May 2007

Additional files

Additional file 1:

Set of 155 bacterial-specific E. coli proteins. Phylogenetic profiles of 155 E. coli proteins, none of which had a homolog in any of the archaeal and eukaryotic genomes (e-value > 1e-2) used in this study. Red and blue colors indicate the presence (lower values in the profile) or absence (higher values in the profile) of a homolog, respectively. For example BLAST e-values 1e-10, 1e-5, 1e-3, 1e-2 and 1e-1 are represented as 0.03, 0.06, 0.10, 0.15, and 0.30, respectively, in profiles (see Materials and Methods).

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