NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST-formatted sequences. The alignment algorithm involves global dynamic programming alignment to a fixed template sequence(s) without any end-gap penalty (think Pearson’s align0 program with a fixed template sequence containing arbitrary gap positions). Non-GATC characters are not recognized and so are treated as ‘A’ characters within the alignment algorithm.
The Broad Institute, Cambridge, MA
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Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW.
Genome Res. 2011 Mar;21(3):494-504. Epub 2011 Jan 6.