Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals

Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals

Bidirectional best hits (BBH), which entails identifying the pairs of genes in two different genomes that are more similar to each other than either is to any other gene in the other genome, is a simple and widely used method to infer orthology. A recent study has analyzed the link between BBH and orthology in bacteria and archaea and concluded that, given the very high consistency in BBH they ...

Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss?

Reciprocal Best Hits (RBH) are a common proxy for orthology in comparative genomics. Essentially, a RBH is found when the proteins encoded by two genes, each in a different genome, find each other as the best scoring match in the other genome. NCBI's BLAST is the software most usually used for the sequence comparisons necessary to finding RBHs. Since sequence comparison can be time consuming, w...

Choosing BLAST options for better detection of orthologs as reciprocal best hits

MOTIVATION The analyses of the increasing number of genome sequences requires shortcuts for the detection of orthologs, such as Reciprocal Best Hits (RBH), where orthologs are assumed if two genes each in a different genome find each other as the best hit in the other genome. Two BLAST options seem to affect alignment scores the most, and thus the choice of a best hit: the filtering of low info...

There's No Such Thing as Best Practice

Diversity of Plants and Animals in Mountain Ecosystems in Tajikistan

Tajikistan is a hotspot of plant and animal species diversity and endemism andis important for the conservation of biodiversity on a global scale. The country is located ata biological crossroads. Species from Central and Northern Europe, Central Asia, theMiddle East, and North Africa mingle here with endemics found nowhere else. Therichness of Tajikistan‘s biodiversity shows up at the genetic,...