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

Abstract:

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 information sequence segments and the algorithm used to produce the final alignment. Thus, we decided to test whether such options would help better detect orthologs. Results: Using Escherichia coli K12 as an example, we compared the number and quality of orthologs detected as RBH. We tested four different conditions derived from two options: filtering of low-information segments, hard (default) versus soft; and alignment algorithm, default (based on matching words) versus Smith–Waterman. All …

Año de publicación:

2008

Keywords:

Fuente:

google