PMID:18042555

Citation	Moreno-Hagelsieb, G and Latimer, K (2008) Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics 24:319-24
Abstract	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.
Links	PubMed Online version:10.1093/bioinformatics/btm585
Keywords	Base Sequence; Chromosome Mapping/methods; DNA, Bacterial/genetics; Database Management Systems; Databases, Genetic; Escherichia coli/genetics; Molecular Sequence Data; Proteins/genetics; Sequence Alignment/methods; Sequence Analysis, DNA/methods; Sequence Homology, Nucleic Acid
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