MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

We developed a new approach based on an algorithm implemented in a freely available program called MACSE that allows the direct alignment of nucleotide sequences from protein-coding genes without disrupting the underlying codon structure even in the presence of frameshifts and/or premature stop-codons. MACSE is the first alignment program that is able to deal with frameshifts caused by sequencing errors and/or other biological sources of frameshifting mutations. As illustrated through biological case study examples, our program will particularly be helpful in aligning sequences of pseudogenes with their functional counterparts, aligning transcriptome sequence reads produced by next-generation sequencing methods to a coding reference, and in pinpointing undetected errors in sequences from public sequence databases.

Reference: Ranwez V., Harispe S., Delsuc F. & Douzery E.J.P. (2011). MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PLoS One 6: e22594.