Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence align...

Assessments of the acceptability of new transplantation practices require a pinpointing of not only the meaning of death, but also the timing of death. They typically perceive elective ventilation as occurring just prior to death and non-heart-beating donor protocols as operative just after death. However, such practices in fact highlight the general vagueness and ambiguity surrounding these is...

Early in their evolution, perhaps during their transition from Agnatha (jawless fish) to Gnathostomata (jawed animals), vertebrates committed as much as 1% of their proteinencoding genome to a new system of defense against parasites (1). Central to this anticipatory (adaptive) immune system (2) are three types of antigen receptor—immunoglobulin (Ig), T cell receptor (Tcr), and major histocompat...

Several recent publications illustrated advantages of using sequence profiles in recognizing distant homologies between proteins. At the same time, the practical usefulness of distant homology recognition depends not only on the sensitivity of the algorithm, but also on the quality of the alignment between a prediction target and the template from the database of known proteins. Here, we study ...

MOTIVATION The success of genome sequencing has resulted in many protein sequences without functional annotation. We present ConFunc, an automated Gene Ontology (GO)-based protein function prediction approach, which uses conserved residues to generate sequence profiles to infer function. ConFunc split sets of sequences identified by PSI-BLAST into sub-alignments according to their GO annotation...

Lanternfish are a relatively small but very abundant fish. They live deep in the ocean’s “twilight” zone where there is not much light. A unique community of lanternfish Southern Ocean, they key part Antarctic food web. also play an important role moving carbon from atmosphere into ocean, it stored. In this article, we explain current knowledge on Ocean lanternfish, including how produce their ...