Fig. 3

The problem of multiply-mapping short-reads, and the FAMLI algorithm schematized. Three hundred and sixty simulated reads were generated from three CDS. These simulated read was aligned against the UniRef100 database, and all CDS with an alignment within 10% identity of the best match were retained. a The read-depth coverage of the three true peptides (top) b evenness filtering is used to remove the least likely to be present references from being considered. The left column is three randomly selected references that are successfully filtered at this step, the right three false references that are not filtered. c The iterative likelihood-based filtering of one randomly selected synthetic read. Each circle represents one remaining aligned reference CDS for this read; the true positive origin reference is in dark green. The length of each line is proportional to the calculated score at this iteration. d The number of CDS per read as a violin plot. After the tenth iteration, only one reference CDS (the correct) remains for this read