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

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...

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 ...

Silent gastro-oesophageal reflux: how much do we miss?

3 Tappin DM, King C, Paton JY. Lower oesophageal pH monitoring-a useful clinical tool. Arch Dis Child 1992;67:146-8. 4 Evans DF, Robertson CS, Ledingham SJ, Kapila L. Oesophageal pH monitoring for gastrooesophageal reflux: a United Kingdom study. J Pediatr Surg 1991;26:682-5. 5 Cucchiara S, Staiano A, Boccieri A, et al. Effects of cisapride on parameters of oesophageal motility and on prolonged...

Silent gastro-oesophageal reflux: how much do we miss?

3 Tappin DM, King C, Paton JY. Lower oesophageal pH monitoring-a useful clinical tool. Arch Dis Child 1992;67:146-8. 4 Evans DF, Robertson CS, Ledingham SJ, Kapila L. Oesophageal pH monitoring for gastrooesophageal reflux: a United Kingdom study. J Pediatr Surg 1991;26:682-5. 5 Cucchiara S, Staiano A, Boccieri A, et al. Effects of cisapride on parameters of oesophageal motility and on prolonged...

Testing the Speed of Usearch and Blat in Comparison to Blast and Determining Their Sensitivity for Detecting Orthologs as Reciprocal Best Hits