We present ALICO (ALIgnment COnstrainted) null set generator: a framework to generate randomized versions of an input multiple sequence alignment that preserve some of its crucial features including its dependence structure. In particular, we show that, on average, ALICO samples approximately preserve the PIDs (percent identities) between every pair of input sequences. At the same time our examples demonstrate that the average k-mer composition of each of the sampled sequences show great resemblance to the k-mer composition of our genomic training data. Of note is that ALICO requires only pairwise alignment training data rather than multiple alignment training data. We demonstrate the utility of ALICO in predicting the correct results returned by the "homology-aware" finders PhyloCon, MEME with conservation prior and PRIORITY-C, as well as by our "naive" finder GibbsMarkov, applied to the MacIsaac orthologous yeast data. Finally, we show that using ALICO sampling derived p-values to combine results from multiple finders often outperforms its best individual component. Supplementary Material is available at www.liebertonline.com/cmb .
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Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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Site | Modification | Modifier | Source | Reference |
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Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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Evidence ID | Analyze ID | File | Description |
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