Genotyping data are used to detect CNVs using multiple algorithms [ 28] and to perform an affected-only parametric linkage analysis.
In a sense, using multiple algorithms to extract the networks and presenting them to the user is a similar approach to that followed by annotation pipelines, such as Microscope [ 27], DIYA [ 28] or BASys [ 29] among others.
Target prediction analyses were performed using multiple algorithms, including miRanda (John et al, 2004), PicTar (Rajewsky and Socci, 2004), and TargetScanS (Lewis et al, 2003).
However, most CNV studies based on SNP array in human and animals used only the PennCNV software (e.g., Bae et al. [ 23]; Hou et al. [ 55]; Glessner et al. [ 56]), although Winchester et al. [ 54] recommended using multiple algorithms on a single dataset to produce the most informative and reliable results.
The same set of upstream sequences was analyzed using another Gibbs-sampler, MEME, with the intent of converging upon a biologically relevant motif using multiple algorithms.
Sixty putative lipoproteins were predicted from the genomic sequence of A. pleuropneumoniae using multiple algorithms.
The Joint Genome Institute JGII) and wFleaBase generated gene models for protein-coding genes in Daphnia pulex using multiple algorithms.
To date, several miR response elements that might target BCRP mRNA 3′-UTR have been identified using multiple algorithms [231], [232].
The RDP3 Beta 27 [ 74] package was used to test for signatures of recombination using multiple algorithms simultaneously: RDP [ 75], GENECONV [ 76], BootScan [ 77], MaxChi [ 78], Chimaera [ 79], and 3Seq [ 80].
