The NcDNAlign pipeline combines pairwise BLAST alignments to create initial MSAs, which are then locally improved and trimmed. The program is optimized for speed and hence is particulary well-suited to pilot studies. We demonstrate the practical use of NcDNAlign in three case studies: the search for ncRNAs in gammaproteobacteria and the analysis of conserved noncoding DNA in nematodes and teleost fish, in the latter case focusing on the fate of duplicated ultra-conserved regions.
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Dominic Rose, Jana Hertel, Kristin Reiche, Peter F Stadler, J?rg Hackermüller
NcDNAlign – Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences
Genomics 92 (2008) 65-74.