alns — A searchable and filterable sequence alignment format

Abstract

Nucleotides and amino acids are basic building units of RNA, DNA and protein. Although intensive studies on understanding how the change of these building blocks affect the phenotypes of these biopolymers are ever increasing, many popular alignment formats are generated by pairwise comparision 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 wide disciplines in knowledge discovery.