To evaluate the performance of RNAstrand on alignments which have not been identified as structured RNA by RNAz, we constructed a second test set which only consists of alignments not classified as structured RNA by RNAz in both reading directions.
It is from dataset that we create the four optimized datasets as summarized in Table 2 and Figure 2. The first dataset, D s, consists of alignments with a single individual sampled per species at each locus (not necessarily the same individual across loci).
The features used by the RAF program, as evaluated in this article, consist of alignment features, and pairing features,.
Up to this stage, the alignment consists of aligned representatives of NCIV clusters.
BAM files, binary versions of Sequence Alignment/Map (SAM) format files, consist of alignments of DNA reads (generally short) to a reference sequence, usually a complete genome.
Real gene alignment protocol consists of strict alignment (Bowtie, no mismatches, single alignment location) to the human genome (hg18, NCBI Build 36.1).
Pseudogene alignment protocol consists of strict alignment (Bowtie, no mismatches, report reads with only one alignment location only) to the composite genome.
The comparison in this section consists of the alignment accuracy and robustness.
For ISAR imaging of a non-cooperative target, a data-driven compensation procedure must be accounted, which generally consists of range alignment and phase adjustment.
Each iteration of the training procedure consists of time alignment by dynamic programming (Viterbi algorithm) followed by parameter estimation, resulting in segmental k-means training procedure [3, 4].
