Clustal W and Clustal X version 2.0
Bioinformatics
An efficient motif discovery algorithm with unknown motif length and number of binding sites
International Journal of Data Mining and Bioinformatics
Clustering sequences by overlap
International Journal of Data Mining and Bioinformatics
Several remarks on the metric space of genetic codes
International Journal of Data Mining and Bioinformatics
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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.