Bioinformatics for DNA Sequence Analysis.pdf - Index of

256 Blanco and AbrilTable 12.2Sensitivity of the predictions in D. yakuba (see Note 16)EXON POSITION1 POSITION2 GENEID yakuba GENSCAN yakuba GENEMARK yakubaE1 184 239 OK NO OKE2 337 1,129 OK OK OKE3 1,289 2,584 OK OK OKE4 2,644 2,861 OK OK OKE5 2,935 3,235 OK OK OKE6 5,119 5,268 OK OK OKE7 5,331 5,746 OK OK OKE8 5,816 6,144 OK OK OKE9 6,200 6,367 OK OK OKE10 6,436 6,529 OK OK OKE11 6,703 6,888 OK OK OKE12 6,952 7,148 OK OK OKE13 7,343 7,363 NO NO NOWe have used the fragments of the protein from D. melanogaster, which possibly constitute the exons ofthe gene, to evaluate the accuracy of the predictions by GENEID, GENSCAN and GENEMARK. Theprotein was aligned previously to the syntenic region in D. yakuba in which the gene should be identified.We can connect to the GENEWISE web server at http://www.ebi.ac.uk/Wise2/ (see Note 15). First, we need to getfrom the UCSC genome browser the translated protein from theRefSeq track in D. melanogaster, and the genomic syntenic regionfrom D. yakuba again. Then, both sequences must be copied intotheir respective boxes in the GENEWISE form to run the program.Let us explore the predictions: the alignment between thecollection of predicted splice sites and the real protein is shownvertically – each column contains the alignment between theamino acids in the input protein and the corresponding codonsin the input genomic region; introns are represented as gaps withinsuch an alignment (Fig. 12.6). GENEWISE alignment is veryaccurate in most exons. Despite the ab initio prediction obtainedin the previous section was not significantly improved, GENE-WISE identified more accurately the location of the internal exonaround the position 5,000, which was wrongly predicted before.On the contrary, the actual terminal exon was not included intothe final alignment (Fig. 12.5).