For the microRNA target prediction, conservation scores were not taken into account.
The input file format (Additional file 1: Table S1) should include the following columns: chromosome number, chromosome coordinate, reference allele, sample allele, gene symbol, transcript ID, nucleotide alteration, amino acid alteration, SIFT functional prediction, PolyPhen-2 functional prediction, conservation phyloP p-value, dbSNP ID, and 1000 genome allele frequency.
Thermodynamic binding energy predictions, conservation and uniqueness scores must be computed for millions of candidate probes, in order to select an optimal combination of probes for each target gene family, balancing sensitivity, specificity, and breadth of coverage.
Detailed information about the predicted miRNAs, including the prediction method, conservation, reference sequences, location in the reference sequences, precursor sequences, hairpin structures, minimum folding free energies, mature sequences and A + U content is available in Additional file 3: Table S1, Additional file 4: Table S2, Additional file 5: Table S3, and Additional file 6: Table S4.
Combining disorder prediction and conservation data, many regions of conserved predicted disorder were found within protein domains.
This approach of improving function sequence prediction from conservation is different from the more common approach of using nucleotide-level conservation, which is sensitive to alignment between orthologous sequences.
Hidden Markov Models are widely used in bioinformatics for applications that range from exon boundary prediction to conservation analyses [39].
Functional prediction and conservation analysis were performed using ANNOVAR.
SLiMSearch for example will rank matches by disorder prediction and conservation [ 71].
An optional rule for target prediction required conservation of the putative binding sites among the same influenza A subtypes.
Table 1 contains a summary of the information pertaining to all 55 candidate sRNAs, including the flanking genes, Rfam prediction, and conservation across other genomes.
