The standardized interface to sequence analysis tools is highly desirable to integrate bioinformatics applications. Currently existing software packages and programming toolkits (BioPerl, BioJava, etc.) used by bioinformaticians for DNA sequence analysis have limited support for exchanging and reusing data. To solve these issues, we propose the Web services approach and discuss how to apply the Web services technology for nucleotide sequence analysis workflow. In this work, we present a program-friendly interface to DNA sequence analysis tools using Web services. All data including query requests to the Web services are managed in XML-formats. The Web services responsible for statistical analysis provide an interface to the R statistical environment and can perform analysis using several statistical methods (including correspondence analysis and principal component analysis). Output of the Web services is in XML-format and, thus, can be stored in local XML databases.