Kangaroo - A pattern-matching program for biological sequences

Background: Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide straightforward or readily available query tools to perform simple searches, such as identifying transcription binding sites, protein motifs, or repetitive DNA sequences. However, in many cases simple pattern-matching searches can reveal a wealth of information. We present in this paper a regular expression pattern-matching tool that was used to identify short repetitive DNA sequences in human coding regions for the purpose of identifying potential mutation sites in mismatch repair deficient cells. Results: Kangaroo is a web-based regular expression pattern-matching program that can search for patterns in DNA, protein, or coding region sequences in ten different organisms. The program is implemented to facilitate a wide range of queries with no restriction on the length or complexity of the query ex...

• Type: Journal
• Year: 2002
• Where: BMCBI
• Authors: Doron Betel, Christopher W. V. Hogue
• Keywords: BMCBI 2002, Dna Sequences, Repetitive Dna Sequences, Sequences