Fast Local Alignment for Gigabases (FLAG) -- an efficient bioinformatics tool for nucleotide sequence comparison

Pei-Ing Hwang, Research Fellow/Consultant

Bioinformatics Department, Molecular Biomedical Technology Division, BioMedical Engineering Center (BMEC), Industrial Technology Research Institute (ITRI), Taiwan

The bioinformatic software, Fast Local Alignment for Gigabases (FLAG), developed at the Bioinformatics Department at BMEC, ITRI, were implemented on a highly efficient but different alignment algorithm from those used in BLAST and FASTA. Based on the benchmark testing results (, FLAGs perform sequence alignment faster and are able to identify potential homology at lower level. FLAG provides a faster and better alternative to those online tools. Two FLAG software are currently available online (1) Cluster FLAG ( performing DNA database searches on a 64-cpu pc-cluster with specially designed post-alignment presentation and (2) Pairwise FLAG doing very fast local comparisons between a pair of DNA sequences ( especially powerful when comparing long ones (>1Mbp). Self FLAG has been used to construct a database of intra-chromosome or intra-genome repeating sequences. Development of more FLAG based applications is in progress.

The design of FLAG from biology aspect, the development of FLAG, its performance, and the potential in genomics research will be shared with the audience.