Related Experiment Video
Updated: Sep 30, 2026

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp
Published on: June 20, 2018
Kangaroo--a pattern-matching program for biological sequences
Doron Betel1, Christopher W V Hogue
1Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada. betel@mshri.on.ca
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 expression. The program is accessible on the web at http://bioinfo.mshri.on.ca/kangaroo/ and the source code is freely distributed at http://sourceforge.net/projects/slritools/.
Conclusion:
A low-level simple pattern-matching application can prove to be a useful tool in many research settings. For example, Kangaroo was used to identify potential genetic targets in a human colorectal cancer variant that is characterized by a high frequency of mutations in coding regions containing mononucleotide repeats.
Related Concept Videos
Multi-species Conserved Sequences
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Evolutionary Relationships through Genome Comparisons
RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Applications of Molecular Taxonomy
Maxam-Gilbert Sequencing
Challenges of the Maxam-Gilbert Method
The...
Sanger Sequencing

