Nucleic Acids Research, 2006, Vol. 34, Web Server issue W655 A novel way of masking or changing a sequence by population-speciﬁc allele frequency is shown in Figure 2D. Here you can see that compared to the original sequence, 2 nt have been replaced (‘C’ to ‘t’ and ‘G’ to ‘a’) because these are the major alleles in Japanese dataset. The major allele frequen- cies of the marked SNPs in Japanese dataset are 1.00 and 0.93, respectively. Both alleles that have been replaced are the major alleles in all other HapMap populations as well. The other SNPs within this sequence remain unchanged because their major allele is already present in the Golden Path sequence or because HapMap database does not contain information about them. PERFORMANCE Major steps in the algorithm are the localization of the sequence by a homology search, the localization of SNPs on the sequence and ﬁnding repeats by RepeatMasker or GenomeMasker. RepeatMasker is generally too slow for real- time masking. Therefore, large genomes are typically pre-masked with RepeatMasker. If the user requests RepeatMasker-masked sequence then the corresponding region is retrieved from the database. We have taken a similar approach by downloading RepeatMasker-masked genome sequences from ENSEMBL database and installed them in a local database. Fortunately, GenomeMasker program is several orders of magnitude faster than RepeatMasker and can thus be executed each time user submits a new masking job. This allows executing it with slightly different options each time, giving the user more ﬂexibility in masking. Queries of dbSNP and HapMap databases and masking with GenomeMasker take only seconds to complete even with large input sizes. The main limiting factor is MEGABLAST execution time for sequences uploaded by the user. Therefore the sequence region masked by our web server is currently limited to a maximum length of 100 000 bp and single sequence per ﬁle, which should take no more than 2.5 min (Table 2). Please contact the authors for masking larger sequences or multiple sequence regions. ACKNOWLEDGEMENTS This work was supported by the Estonian Ministry of Education and Research grant 0182649s04, grant 6041 from Estonian Science Foundation and grant EU19730 from Enterprise Table 2. The performance of SNPmasker for different tasks Job Sequence from FASTA file No repeat-masking, SNPs masked with ‘N’ No repeat-masking, SNPs masked using HapMap allele frequency GenomeMasker, SNPs masked with ‘N’ RepeatMasker, SNPs masked with ‘N’ Sequence defined by chromosomal coordinates No repeat-masking, SNPs masked with ‘N’ No repeat-masking, SNPs masked using HapMap allele frequency GenomeMasker, SNPs masked with ‘N’ RepeatMasker, SNPs masked with ‘N’ 1 kb 10 kb 100 kb 32 s 32 s 38 s 32 s 14 s 14 s 15 s 14 s 35 s 35 s 40 s 35 s 14 s 14 s 15 s 14 s 142 s 146 s 148 s 142 s 14 s 17 s 18 s 14 s Estonia. The authors thank To˜ nis Org, Elin Lo˜ hmussaar and Neeme To˜ nisson for a critical reading of the manuscript, and Katre Palm and Signe Sumerik for a valuable help with English grammar. Funding to pay the Open Access publication charges for this article was provided by the Estonian Ministry of Education and Research grant 0182649s04. Conflict of interest statement. None declared. REFERENCES 1. Syvanen,A.C. (2005) Toward genome-wide SNP genotyping. Nature Genet., 37, S5–S10. 2. Koboldt,D.C., Miller,R.D. and Kwok,P.Y. (2006) Distribution of human SNPs and its effect on high-throughput genotyping. Hum. Mutat., 27, 249–254. 3. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402. 4. Sherry,S.T., Ward,M.H., Kholodov,M., Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308–311. 5. Andreson,R., Reppo,E., Kaplinski,L. and Remm,M. (2006) GenomeMasker package for designing unique genomic PCR primers. BMC Bioinformatics, 7, 172. 6. Birney,E., Andrews,D., Caccamo,M., Chen,Y., Clarke,L., Coates,G., Cox,T., Cunningham,F., Curwen,V., Cutts,T. et al. (2006) Ensembl 2006. Nucleic Acids Res., 34, D556–D561. 7. Altshuler,D., Brooks,L.D., Chakravarti,A., Collins,F.S., Daly,M.J. and Donnelly,P. (2005) A haplotype map of the human genome. Nature, 437, 1299–1320. 8. Zhang,Z., Schwartz,S., Wagner,L. and Miller,W. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol., 7, 203–214.