Low complexity filtering

The server does not filter your query sequence for low compositional complexity regions by default. Low complexity regions commonly give spuriously high scores that reflect compositional bias rather than significant position-by- position alignment. Filtering can elminate these potentially confounding matches (e.g., hits against proline-rich regions or poly-A tails) from the blast reports, leaving regions whose blast statistics reflect the specificity of their pairwise alignment. Queries searched with the blastn program are filtered with DUST. Other programs use SEG.

Low complexity sequence found by a filter program is substituted using the letter "N" in nucleotide sequence (e.g., "NNNNNNNNNNNNN") and the letter "X" in protein sequences (e.g., "XXXXXXXXX"). Users may turn on filtering by checking the Low complexity box.

Reference for the DUST program:

Tatusov, R. L. and D. J. Lipman, in preparation.
Hancock, J. M. and J. S. Armstrong (1994). SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences. Comput Appl Biosci 10:67-70.

Reference for the SEG program:

Wootton, J. C. and S. Federhen (1993). Statistics of local complexity in amino acid sequences and sequence databases. Computers in Chemistry 17:149-163.
Wootton, J. C. and S. Federhen (1996). Analysis of compositionally biased regions in sequence databases. Methods in Enzymology 266: 554-571.

Reference for the role of filtering in search strategies:

Altschul, S. F., M. S. Boguski, W. Gish, J. C. Wootton (1994). Issues in searching molecular sequence databases. Nat Genet 6: 119-129.