PSI-BLAST is an iterative program to search a database for proteins with distant similarity to
a query sequence. We investigated over a dozen modifications to the methods used in PSI-…

▪ Abstract Comparative analysis of bacterial, archaeal, and eukaryotic genomes indicates
that a significant fraction of the genes in the prokaryotic genomes have been subject to …

Background The CRISPR-Cas adaptive immunity systems that are present in most Archaea
and many Bacteria function by incorporating fragments of alien genomes into specific …

A previous comparative-genomic study of large nuclear and cytoplasmic DNA viruses (NCLDVs)
of eukaryotes revealed the monophyletic origin of four viral families: poxviruses, …

The regulatory interactions between transcription factors and their target genes can be
conceptualised as a directed graph. At a global level, these regulatory networks display a scale-…

The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage
caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic …

DNA cytosine methylation is crucial for retrotransposon silencing and mammalian development.
In a computational search for enzymes that could modify 5-methylcytosine (5mC), we …

Analysis of the 1,042,519–base pair Chlamydia trachomatis genome revealed unexpected
features related to the complex biology of chlamydiae. Although chlamydiae lack many …

Using a combination of computer methods for iterative database searches and multiple
sequence alignment, we show that protein sequences related to the AAA family of ATPases are …

NF-κB transcription factors mediate the effects of pro-inflammatory cytokines such as tumour
necrosis factor-α and interleukin-1β 1 . Failure to downregulate NF-κB transcriptional activity …