“ What is “low-complexity” sequence? Regions with low-complexity sequence have an unusual composition that can create problems in sequence similarity searching. For amino acid queries this compositional bias is determined by the SEG program (Wootton and Federhen, 1996). For nucleotide queries it is determined by the DustMasker program (Morgulis, et al., 2006). Low-complexity sequence can often be recognized by visual inspection. For example, the protein sequence PPCDPPPPPKDKKKKDDGPP has low complexity and so does the nucleotide sequence AAATAAAAAAAATAAAAAAT. Filters are used to remove low-complexity sequence because it can cause artifactual hits. In BLAST searches performed without a filter, high scoring hits may be reported only because of the presence of a low-complexity region. Most often, it is inappropriate to consider this type of match as the result of shared homology. Rather, it is as if the low-complexity region is “sticky” and is pulling out many sequences that are not truly related.
August 6, 2009
