- Open Access
Erratum to: Benchmarking tools for the alignment of functional noncoding DNA
© Pollard et al; licensee BioMed Central Ltd. 2004
Received: 11 May 2004
Accepted: 08 June 2004
Published: 08 June 2004
The original article was published in BMC Bioinformatics 2004 5:6
The true overall alignment coverage for BLASTZ with and without insertion/deletion evolution and with and without blocks of constraint is shown in Figure 1, and reveals increased overall coverage in the presence of constrained blocks for intermediate to high divergence distances (Figures 1C & 1D) relative to previous results ( Figure 3C & 3D). As a consequence, the true overall sensitivity for BLASTZ is increased for intermediate to high divergence distances, especially in the presence of insertion/deletion evolution and constrained blocks (Figure 2D) relative to previous results ( Figure 4D).
The most important revisions to  concern BLASTZ performance in interspersed blocks of constrained sequences (Figures 3, 4). Figure 3 shows that the true constraint coverage, and therefore constraint sensitivity, of BLASTZ is much improved relative to previous results for intermediate to high divergence distances ( Figure 5). Thus BLASTZ has increased constraint coverage relative to overall coverage (cp. Figures 1C &1D with 3A &3B), indicating that BLASTZ local alignments preferentially occur in constrained sequences for intermediate to high divergence distances, overturning claims on page 6 of  to the contrary. Likewise, the claim that BLASTZ has a "dramatic decrease in constraint sensitivity in the presence of indel evolution" on page 10 of  is incorrect. The increase in overall coverage, however, decreases the constraint specificity of BLASTZ for intermediate to high divergence distances (Figure 4A &4B) relative to previous results ( Figure 6A & 6B). This decrease in constraint specificity requires reconsideration of the use of BLASTZ local alignments as specific detectors of constrained noncoding sequences discussed page 10 of .
Revised performance statistics for BLASTZ are posted along with previous results at . We apologize for any misconception or inconvenience this error may have caused.
- Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB: Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 2004, 5: 6-. 10.1186/1471-2105-5-6PubMed CentralView ArticlePubMedGoogle Scholar
- Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W: Human-mouse alignments with BLASTZ. Genome Res 2003, 13: 103–7. 10.1101/gr.809403PubMed CentralView ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.