Rosetta

[…] of slam consist of a splice-site detector, an intron/intergene model, an exon pair scoring model, and a conserved noncoding sequence model. the accuracy of the technique is validated on the rosetta testset of 117 single-gene sequences as well as multigene lloxa cluster. slam compares favorably to other gene finders including genscan , rosetta , sgp-1 , sgp-2 , twin-scan , particularly […]

[…] together with the genome of a suitably related species (e.g., mouse), one can combine the conserved information of the two species to develop a more refined probability models for the gene portions (rosetta [], cem [], twinscan [], slam [], and sgp2 [–]). while these approaches have been effective in predicting genes, a noticeable drawback is that the more refined a probability model is, […]

[…] comparison with genomic sequences of reference species, capturing phylogenetic footprints, as coding sequences tend to be relatively highly conserved. reference-based gene finders such as dps [], rosetta [], procrustes [], genomescan [], projector [], genewise [], genemapper [] and exonhunter [] have sought to predict genes in target species through alignment with genes or proteins […]

[…] study the conservation across them [,]. recently, a new class of gene-prediction algorithms which exploits the power of comparative genomics have been developed, these include but are not limited to rosetta [], cem [], twinscan [], slam [], and sgp2 []. relative to the single genome approaches, these programs have substantially reduced the number of false predictions, (i.e. improved […]

[…] these approaches are multiple expectation maximisation for motif elicitation (meme) and gibbs sampling [-]., one application of multi-genome alignment is to improve the efficiency of gene finding. rosetta reconstructs co-linear gene structures from global alignments and defines exons as sub-sequences bounded by splice sites []. syntenic gene prediction version 1 (sgp18) reconstructs genes […]