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In addition, even though the STOOP technique has been generally proposed to be applied from sequence diagrams, the technique itself works on an internal model that combines the diagrams.
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To demonstrate that BigFoot can be applied to sequence data from vertebrates, we analyzed a 256 base pair region previously identified as the major regulatory element of human α-globin (αMRE) [ 40].
While our method has been developed for 16S rRNA sequencing data from human body, it can be applied to 16S sequencing data from other organisms.
Probe designed using this option can be applied in detecting sequences from samples with mixed genomes or transcriptomes such as specimens in a metagenomic study.
Our approach can be applied to different sequencing data sets generated from different platforms.
BATS identifies the sequences where comparative modelling techniques can be applied, by choosing template sequences from the BLAST output file using their scores, expectation values, identity and sequence similarity as criteria.
The common PCR primer pairs designed by our algorithm could be applied to amplify conserved sequences of genes from the same or different organisms.
The latest InterPro [ 23] database that represents a collection of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences was downloaded from the website of European Bioinformatics Institute and was compared with our unigenes using BLASTX with E-value≤1e-5.
The procedure can be applied to probabilities calculated from pure sequence or pure structure or combined sequence and structure.
Although our GMM method might be applied to predict copy number from sequencing read-depth, it was not developed to this aim.
Although our analysis here focuses on microarray expression profiles, we speculate that ISOpure could be applied directly to abundance estimates from sequencing (RNA-seq) data.
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