|
| Name | URL | Feature | Prediction algorithm |
|
| Tilling array [47] | http://www.genomebiology.com/2014/15/3/R48 | Synonymous amino acid substitutions, reading frame conservation, and the occurrence of premature stop codons | RNAcode algorithm and biweight kernels |
|
| DigitagCT [48] | http://cractools.gforge.inria.fr/softwares/digitagct | Genomic sequences, DGE tags, and tiling array expression | Infernal and BLASTN |
|
| BlockClust [49] | http://toolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow | (1) The block group: entropy of read starts, entropy of read ends, entropy of read lengths, median of normalized read expressions and normalized read expression levels in first quantile; (2) block: number of multimapped reads, entropy of read lengths, entropy of read expressions, minimum read length and block length, and (3) block edge: contiguity and difference in median read expressions | Graph-kernel SVM |
|
| Noncoder [50] | http://noncoder.mpi-bn.mpg.de/ | Sequence homology, evolutionary information, the longest reading frame in three forward frames, log-odds score, coverage of the predicted orf, and integrity of the predicted orf | BLAT and PhyloCSF |
|
| Vicinal [51] | http://nar.oxfordjournals.org/content/42/9/e79.full.pdf+html | Chimeric RNA-cDNA fragments and terminal stem-loop | Bowtie 2 local mapping, filtering, and Vicinal mapping |
|
| CoRAL [52] | http://nar.oxfordjournals.org/content/41/14/e137.full.pdf+html | Read length, abundance of antisense transcription, 5′ and 3′ positional entropy, four nucleotide frequencies transformed into a log-odds ratio relative to equal base frequencies, and MFE | Multiclass classification random forest |
|
| FlaiMapper [53] | http://www.ncbi.nlm.nih.gov/pubmed/25338717 | Densities of start and end positions of aligned reads and read lengths | Peak detection on the start and end position densities followed by filtering and a reconstruction process |
|
