Home LiteratureArticle Details
PMID: 16845091 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.

Nucleic acids research ·Vol. 34 ·No. Web Server issue ·2006-07-01 ·Pages W651-5

Andreson R, Puurand T, Remm M

Abstract

SNPmasker is a comprehensive web interface for masking large eukaryotic genomes. The program is designed to mask SNPs from recent dbSNP database and to mask the repeats with two alternative programs. In addition to the SNP masking, we also offer population-specific substitution of SNP alleles in genomic sequence according to SNP frequencies in HapMap Phase II data. The input to SNPmasker can be defined in chromosomal coordinates or inserted as a sequence. The sequences masked by our web server are most useful as a preliminary step for different primer and probe design tasks. The service is available at http://bioinfo.ebc.ee/snpmasker/ and is free for all users.

MeSH Terms
Alleles Animals DNA Primers Databases, Nucleic Acid Genome, Human Genomics/methods Humans Internet Mice Nucleic Acid Probes Polymorphism, Single Nucleotide Repetitive Sequences, Nucleic Acid Software User-Computer Interface
Chemicals
DNA Primers Nucleic Acid Probes
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Andreson Reidar
Department of Bioinformatics, University of Tartu, Estonia.
Puurand Tarmo
Remm Maido
References (8)
8 references, click to expand
  1. A greedy algorithm for aligning DNA sequences.
    J Comput Biol. 2000 Feb-Apr;7(1-2):203-14 PMID: 10890397
  2. dbSNP: the NCBI database of genetic variation.
    Nucleic Acids Res. 2001 Jan 1;29(1):308-11 PMID: 11125122
  3. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  4. GENOMEMASKER package for designing unique genomic PCR primers.
    BMC Bioinformatics. 2006;7:172 PMID: 16566824
  5. A haplotype map of the human genome.
    Nature. 2005 Oct 27;437(7063):1299-320 PMID: 16255080
  6. Ensembl 2006.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D556-61 PMID: 16381931
  7. Distribution of human SNPs and its effect on high-throughput genotyping.
    Hum Mutat. 2006 Mar;27(3):249-54 PMID: 16425292
  8. Toward genome-wide SNP genotyping.
    Nat Genet. 2005 Jun;37 Suppl:S5-10 PMID: 15920530
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl125
Published
2006-07-01
Pages
W651-5
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1538889
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkl125 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2