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Lempel-Ziv complexity is the basis for widely used compression algorithms. It has also been proposed as the basis for a distance metric to measure evolutionary distance. In this work we present an extension of the latter idea to develop a low complexity robust species-specific genomic signature. This signature can be used to identify biological organisms using only a small fragment of their genome...
Average mutual information (AMI) has been applied to many fields, including various aspects of bioinformatics. In this paper, we evaluate its performance as a measure of evolutionary distance between sequences. We use the internal transcribed spacer (ITS) regions for 16 fungal sequences as representative sequences used for species comparison. We generate profiles based on the AMI for each species'...
Bulk segregation analysis mapping is a widely used approach in functional genomics, especially now that low sequencing costs make mapping-by-sequencing realistic. However, the huge data processing required is not trivial. To help in this regard, we utilized our population of maize kernel mutants to develop a new mapping-by-sequencing analysis software tool, (MSA), to identify causative genes based...
DNA methylation and histone modifications form the epigenetic code. Cytosine methylation maintains an inactive-condensed chromatin state and is involved in many cellular events such as gene expression, chromosomal stability, cell differentiation, and carcinogenesis. CpG islands (CGIs), which are stretches of DNA in vertebrate organisms with an over-representation of the CpG dinucleotide, are naturally...
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