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...

Tan et al. (1) comment on our earlier paper regarding the accuracy of multiple sequence alignments (MSAs) using different guide tree topologies (2). We stress that the scope of our result was confined to alignments of very large numbers of protein sequences with known structures, where accuracy was measured against structure-based alignments. We point out that this result could not be translate...

UNLABELLED PREMISE OF THE STUDY Phylogenetic analysis of DNA and amino acid sequences requires the creation of files formatted specifically for each analysis package. Programs currently available cannot simultaneously code inferred insertion/deletion (indel) events in sequence alignments and concatenate data sets. • METHODS AND RESULTS A novel Perl script, 2matrix, was created to concatena...

A long-time observation in genomes from bacteria to humans is that the level of nucleotide diversity varies from region to region within the genome. The sequence at some spots is virtually identical among all individuals in a population, while at other spots, variation abounds. What accounts for this differential variability from place to place within the genome? In this issue of PloS Biology, ...

FRAMESHIFTING RESULTS FROM TWO MAIN MECHANISMS: genomic insertions or deletions (indels) or programmed ribosomal frameshifting. Whereas indels can disrupt normal protein function, programmed ribosomal frameshifting can result in dual-coding genes, each of which can produce multiple functional products. Here, I summarize technical advances that have made it possible to identify programmed riboso...

The advent of next generation gene editing technologies has revolutionized the fields of genome engineering in allowing the generation of gene knockout models and functional gene analysis. However, the screening of resultant clones remains challenging due to the simultaneous presence of different indels. Here, we present CRISP-ID, a web application which uses a unique algorithm for genotyping u...