Title: Alns: a new searchable and filterable sequence alignment format

Authors: Ross K.K. Leung; Stephen K.W. Tsui

Addresses: Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong ' Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong

Abstract: Nucleotides and amino acids are basic building units of RNA, DNA and protein. Although intensive studies on understanding how changes in these building blocks affect the phenotypes of these biopolymers are ever increasing, many popular alignment formats are generated by pair-wise comparison tools such as the Basic Local Alignment Search Tool (BLAST). These alignments are user-friendly to researchers but are not convenient for searching, filtering and storage, in particular when there are thousands of alignments generated from highly conserved sequences. Here, we introduce a new alignment format, alns, to facilitate rapid and convenient association of genetic changes and similarity to other sources of information such as phenotypes, disease state, time, geography and taxonomy via simple spreadsheet functions. The format shall assist biologists from a wide range of disciplines in knowledge discovery.

Keywords: sequence alignment format; alns; bioinformatics; searching; filtering; storage; nucleotides; amino acids; RNA; DNA; proteins.

DOI: 10.1504/IJDMB.2013.053193

International Journal of Data Mining and Bioinformatics, 2013 Vol.7 No.2, pp.135 - 145

Received: 04 Apr 2011
Accepted: 04 Apr 2011
Published online: 20 Oct 2014 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article