XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences

Background: Biological sequence repeats arranged in tandem patterns are widespread in DNA and proteins. While many software tools have been designed to detect DNA tandem repeats (TRs), useful algorithms for identifying protein TRs with varied levels of degeneracy are still needed. Results: To address limitations of current repeat identification methods, and to provide an efficient and flexible algorithm for the detection and analysis of TRs in protein sequences, we designed and implemented a new computational method called XSTREAM. Running time tests confirm the practicality of XSTREAM for analyses of multi-genome datasets. Each of the key capabilities of XSTREAM (e.g., merging, nesting, long-period detection, and TR architecture modeling) are demonstrated using anecdotal examples, and the utility of XSTREAM for identifying TR proteins was validated using data from a recently published paper. Conclusion: We show that XSTREAM is a practical and valuable tool for TR detection in protein...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Aaron M. Newman, James B. Cooper
• Keywords: Biological Sequences, BMCBI 2007, Proteins, XSTREAM