Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons-1

1363 signals) and red (positive M values; IL1403 signals) channels. A: non-normalized data. B: grid-based Lowess normalization. C: S-Lowess normalization based on the LCG set obtained from the comparison of IL1403 amplicon sequences to the ORFs of three strains. D: S-Lowess normalization with a stringent LCG set (99% identity over 100 bp).<p><b>Copyright information:</b></p><p>Taken from "Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons"</p><p>http://www.biomedcentral.com/1471-2105/9/93</p><p>BMC Bioinformatics 2008;9():93-93.</p><p>Published online 11 Feb 2008</p><p>PMCID:PMC2275246.</p><p></p

Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons-3

Ree strains. The Rvalues indicate the quality of the regression curve fit (where higher is better).<p><b>Copyright information:</b></p><p>Taken from "Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons"</p><p>http://www.biomedcentral.com/1471-2105/9/93</p><p>BMC Bioinformatics 2008;9():93-93.</p><p>Published online 11 Feb 2008</p><p>PMCID:PMC2275246.</p><p></p

Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons-4

Array dataset with the LCGs. In case that for phase 1 prediction of LCGs is selected, the user has to upload microarray feature sequences and select (multiple) genomes (in this study 3 genomes). The optimal parameters for selection of LCGs from a sequence comparison using BLAT of array features versus multiple reporter genomes are difficult to predict. Therefore, selection of a LCG set is facilitated by cycling through a maximum of 2 parameters. These parameters are (a combination of two): (i) alignment length cutoff, (ii) E-value cutoff, (iii) percentage nucleotide identity cutoff, (iv) maximum number of hits within the same genome (to account for paralogous genes or duplicated genome fragments), (v) minimum number of hits across genomes (to account for gene conservation in multiple genome sequences). Those array feature sequences meeting the criteria (here in at least 2 out of three genomes a significant BLAT hit; one hit over at least 100 bp with at least 80% nucleotide identity) are marked as LCG and added to the conserved array feature list. In phase 2, the LCGs are used to normalize an uploaded aCGH microarray dataset. The result of phase 2 is a normalized dataset and diagnostic plots.<p><b>Copyright information:</b></p><p>Taken from "Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons"</p><p>http://www.biomedcentral.com/1471-2105/9/93</p><p>BMC Bioinformatics 2008;9():93-93.</p><p>Published online 11 Feb 2008</p><p>PMCID:PMC2275246.</p><p></p

Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons-0

Array dataset with the LCGs. In case that for phase 1 prediction of LCGs is selected, the user has to upload microarray feature sequences and select (multiple) genomes (in this study 3 genomes). The optimal parameters for selection of LCGs from a sequence comparison using BLAT of array features versus multiple reporter genomes are difficult to predict. Therefore, selection of a LCG set is facilitated by cycling through a maximum of 2 parameters. These parameters are (a combination of two): (i) alignment length cutoff, (ii) E-value cutoff, (iii) percentage nucleotide identity cutoff, (iv) maximum number of hits within the same genome (to account for paralogous genes or duplicated genome fragments), (v) minimum number of hits across genomes (to account for gene conservation in multiple genome sequences). Those array feature sequences meeting the criteria (here in at least 2 out of three genomes a significant BLAT hit; one hit over at least 100 bp with at least 80% nucleotide identity) are marked as LCG and added to the conserved array feature list. In phase 2, the LCGs are used to normalize an uploaded aCGH microarray dataset. The result of phase 2 is a normalized dataset and diagnostic plots.<p><b>Copyright information:</b></p><p>Taken from "Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons"</p><p>http://www.biomedcentral.com/1471-2105/9/93</p><p>BMC Bioinformatics 2008;9():93-93.</p><p>Published online 11 Feb 2008</p><p>PMCID:PMC2275246.</p><p></p