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In JoVE (1)
Other Publications (4)
Articles by Jason Bechtel in JoVE
JoVE General
Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA
Department of Medicine, University of Toledo Health Science Campus
We present a public computational web site for the analysis of genomic sequences. It detects DNA sequence patterns with various non-random nucleotide compositions. This resource also generates randomized sequences with diverse levels of complexity.
Other articles by Jason Bechtel on PubMed
Genomic Mid-range Inhomogeneity Correlates with an Abundance of RNA Secondary Structures
Genomes possess different levels of non-randomness, in particular, an inhomogeneity in their nucleotide composition. Inhomogeneity is manifest from the short-range where neighboring nucleotides influence the choice of base at a site, to the long-range, commonly known as isochores, where a particular base composition can span millions of nucleotides. A separate genomic issue that has yet to be thoroughly elucidated is the role that RNA secondary structure (SS) plays in gene expression.
The Alternative Splicing Mutation Database: a Hub for Investigations of Alternative Splicing Using Mutational Evidence
Some mutations in the internal regions of exons occur within splicing enhancers and silencers, influencing the pattern of alternative splicing in the corresponding genes. To understand how these sequence changes affect splicing, we created a database of these mutations.
Calculation of Splicing Potential from the Alternative Splicing Mutation Database
The Alternative Splicing Mutation Database (ASMD) presents a collection of all known mutations inside human exons which affect splicing enhancers and silencers and cause changes in the alternative splicing pattern of the corresponding genes.
Evolution of Genomic Sequence Inhomogeneity at Mid-range Scales
Mid-range inhomogeneity or MRI is the significant enrichment of particular nucleotides in genomic sequences extending from 30 up to several thousands of nucleotides. The best-known manifestation of MRI is CpG islands representing CG-rich regions. Recently it was demonstrated that MRI could be observed not only for G+C content but also for all other nucleotide pairings (e.g. A+G and G+T) as well as for individual bases. Various types of MRI regions are 4-20 times enriched in mammalian genomes compared to their occurrences in random models.
