Characterizing indels

Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins.

Proteins evolve through point mutations as well as by insertions and deletions (indels). During the last decade it has become apparent that protein regions that do not fold into three-dimensional structures, i.e. intrinsically disordered regions, are quite common. Here, we have studied the relationship between protein disorder and indels using HMM-HMM pairwise alignments in two sets of ortholog...

Characterizing sub-topical functions

In this paper, we first give a characterization of sub-topical functions with respect to their lower level sets and epigraph. Next, by using two different classes of elementary functions, we present a characterization of sub-topical functions with respect to their polar functions, and investigate the relation between polar functions and support sets of this class of functions. Finally, we obtai...

Evolutionary Implications of Matk Indels in Poaceae1

Insertion/deletion events (indels) and nucleotide substitutions at the extreme 39 end of the chloroplast gene matK have been identified that distinguish certain major lineages of grasses. A 1-bp (base pair) deletion creating a shift in the open reading frame (ORF) and a point mutation support the positions of Streptochaeta and Anomochloa as the two most basal lineages in Poaceae. Another 1-bp d...

Genomic Distance with DCJ and Indels

The double cut and join (DCJ) operation, introduced by Yancopoulos, Attie and Friedberg in 2005, allows one to represent most rearrangement events in genomes. However, a DCJ cannot perform an insertion or a deletion and most approaches under this model consider only genomes with the same content and without duplications, including the linear time algorithms to compute the DCJ distance and to fi...

Characterizing Physicochemical Properties of Enset Starch