Revised ms : BIOINF - 2003 - 0817 Bellerophon ; a program to detect chimeric sequences in multiple sequence alignments

Summary: Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. 5 Availability: Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl Contact: [email protected] INTRODUCTION 10 A PCR-generated chimeric sequence is usually comprised of two phylogenetically distinct parent sequences and occurs when a prematurely terminated amplicon reanneals to a foreign DNA strand, and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the conversion, recombination or break point. Chimeras are problematic in culture15 independent surveys of microbial communities because they suggest the presence of nonexistent organisms (von Wintzingerode et al., 1997). Several methods have been developed for detecting chimeric sequences (Cole et al., 2003; Komatsoulis and Waterman, 1997; Liesack et al., 1991; Robinson-Cox et al., 1995) that generally rely on direct comparison of individual sequences to one or two putative parent sequences at a 20 time. Here we present an alternative approach based on how well sequences fit into their complete phylogenetic context. METHOD Bellerophon detects chimeras based on a partial treeing approach (Wang and Wang, 1997; Hugenholtz and Huber, 2003), that is, phylogenetic trees are inferred from independent regions (fragments) of a multiple sequence alignment and the branching patterns are compared for incongruencies that may be indicative of chimeric sequences. 5 No trees are actually built during the procedure and the only calculations required are distance (sequence similarity) calculations. A full matrix of distances (dm) between all pairs of sequences are calculated for fragments left and right of an assumed break point. The total absolute deviation of the distance matrices (distance matrix error dme) of n sequences is then 10