Table 1.
The 20 mammals from the EMBL database used in the phylogenetic experiments. The accession number is given on the last column.
Table 2.
The genomic sequence information of three vibrio pathogens consisting of two circular chromosomes.
Figure 1.
The precision-recall curves of the state of the art aligners versus the precision-recall curve of the two LRD aligners, when 10,000 contaminated reads of length 100 from the orangutan are included.
The two variants of the BOWTIE aligner are based on local and global alignment, respectively. The LRD aligner based on hash tables is a fast approximate version of the original LRD aligner.
Table 3.
Several statistics of the state of the art aligners versus the LRD aligner, when 10,000 contaminated reads of length 100 sampled from the orangutan genome are included.
Table 4.
Metrics of the human reads mapped to the human mitochondrial genome (true positives) by the hash LRD aligner versus the human reads that are not mapped to the genome (false negatives).
Figure 2.
The precision-recall curves of the state of the art aligners versus the precision-recall curves of the two LRD aligners, when 50,000 contaminated reads of length 100 from 5 mammals are included.
The two variants of the BOWTIE aligner are based on local and global alignment, respectively. The LRD aligner based on hash tables is a fast approximate version of the original LRD aligner.
Table 5.
Several statistics of the state of the art aligners versus the LRD aligner, when contaminated reads of length
sampled from the genomes of 5 mammals are included.
Table 6.
The recall at best precision of the state of the art aligners versus the LRD aligner, when contaminated reads of length
sampled from the orangutan genome are included.
Table 7.
The recall at best precision of the state of the art aligners versus the LRD aligner, when contaminated reads of length
sampled from the blue whale, the harbor seal, the donkey, and the house mouse genomes are included, respectively.
Table 8.
The results for the real-word setting experiment on mammals.
Table 9.
The results for the hard setting experiment on mammals.
Table 10.
The running times of the BWA aligner, the BLAST aligner, the BOWTIE aligner and the LRD aligner.
Table 11.
The results of the rank-based aligner on vibrio species.
Figure 3.
Local Rank Distance computed in the presence of different types of DNA changes such as point mutations, indels and inversions.
In the first three cases (a), (b) and (c), a single type of DNA polymorphism is included in the second (bottom) string. The last case (d) shows how LRD measures the differences between the two DNA strings when all the types of DNA changes occur in the second string. The nucleotides affected by changes are marked with bold. To compare the results for the different types of DNA changes, the first string is always the same in all the four cases. Note that in all the four examples, LRD is based on 1-mers. In each case, .
Table 12.
Algorithm 1. The hash LRD aligner algorithm.