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Applications from the Mibench benchmark suite were analyzed in terms of cost function for different heuristics considering simulation in different branches.
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The raw microarray data obtained from Microarray Suite v5.0 software were analyzed using a two-sided t-test corrected for unequal variances (Welch test) to compare the mean expression level for each gene between the two groups.
The 100 contigs with the highest number of reads and contigs 1-10,000 as produced by SeqMan 7 (Lasergene Suite 7.0, 2009) were analyzed yielding 600 contigs containing at least one high confidence SNP.
High-resolution chip images were analyzed using Microarray Suite Version 4 (Affymetrix).
Arrays were analyzed using Microarray Suite 5.0 to obtain Absent/Present calls and filtered for transcripts that were not expressed in any experiment.
The resulting image files were analyzed using Affymetrix Microarray Suite 5.1 to generate.CEL files containing the probe level intensities and the x, y coordinates of each probe on the array.
Sequences were analyzed using a suite of bioinformatic applications available at the GreenePortal website (http://tako.cpmc.columbia.edu/Tools), including FASD, a method whereby the statistical distribution of oligonucleotide frequencies within an unknown sequence set is compared to frequencies calculated for known sequence sets.
Images were analyzed using Microarray Suite 4.0 (Affymetrix).
Images were analyzed using softWoRx Suite and softWoRx Explorer software (AppliedPrecision, Issaquah, WA, USA).
The image files obtained were analyzed using Microarray Suite 3.0 software (Affymetrix).
Tandem mass spectra were analyzed using a suite of custom-developed bioinformatics tools.
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