Suite of Tools for Statistical N-Gram Language Modeling for Pattern Mining in Whole Genome Sequences

Ganapathiraju, Madhavi K.; Mitchell, Asia; Mohamed, Thahir; Motwani, Kamiya; Ananthasubramanian, Seshan

doi:10.1142/s0219720012500163

Cited by 4 publications

(4 citation statements)

References 47 publications

(31 reference statements)

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“…We used the Biological Language Modelling Toolkit (BLMT) (version 2) to identify palindromes in the human genomes [20]. BLMT pre-processes the whole genome sequence into suffix arrays and then computes the longest common prefix array, which make searching for patterns like palindromes very efficient.…”

Section: Methodsmentioning

confidence: 99%

A pilot study on the prevalence of DNA palindromes in breast cancer genomes

et al. 2016

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BackgroundDNA palindromes are a unique pattern of repeat sequences that are present in the human genome. It consists of a sequence of nucleotides in which the second half is the complement of the first half but appearing in reverse order. These palindromic sequences may have a significant role in DNA replication, transcription and gene regulation processes. They occur frequently in human cancers by clustering at specific locations of the genome that undergo gene amplification and tumorigenesis. Moreover, some studies showed that palindromes are clustered in amplified regions of breast cancer genomes especially in chromosomes (chr) 8 and 11. With the large number of personal genomes and cancer genomes becoming available, it is now possible to study their association to diseases using computational methods. Here, we conducted a pilot study on chromosomes 8 and 11 of cancer genomes to identify computationally the differentially occurring palindromes.MethodsWe processed 69 breast cancer genomes from The Cancer Genome Atlas including serum-normal and tumor genomes, and 1000 Genomes to serve as control group. The Biological Language Modelling Toolkit (BLMT) computes palindromes in whole genomes. We developed a computational pipeline integrating BLMT to compute and compare prevalence of palindromes in personal genomes.ResultsWe carried out a pilot study on chr 8 and chr 11 taking into account single nucleotide polymorphisms, insertions and deletions. Of all the palindromes that showed any variation in cancer genomes, 38% of what were near breast cancer genes happened to be the most differentiated palindromes in tumor (i.e. they ranked among the top 25% by our heuristic measure).ConclusionsThese results will shed light on the prevalence of palindromes in oncogenes and the mutations that are present in the palindromic regions that could contribute to genomic rearrangements, and breast cancer progression.

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Section: Methodsmentioning

confidence: 99%

A pilot study on the prevalence of DNA palindromes in breast cancer genomes

et al. 2016

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“…With the advent of high-throughput technologies for sequencing personal genomes, the computational question can be revisited not only to find the locations of palindromes in the reference genome but also to study the variations exhibited across individuals. We have developed a suite of tools called the Biological Language Modeling Toolkit (BLMT, version 2) for pattern mining in a genome sequence 31 . The tools in BLMT preprocess the genome sequence into a suffix array that is augmented with other data arrays for mining genomic patterns, including palindromes.…”

Section: Palindromic Variations In Disease Susceptibility Locimentioning

confidence: 99%

“…We employed the BLMT (version 2) 31 to identify palindromes and near-palindromes in the individual human genomes. BLMT preprocesses each wholegenome sequence into a suffix array and then computes the longest common prefix array and rank array, thus making pattern searches very efficient.…”

Section: Palindrome Computation With Blmtmentioning

confidence: 99%

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A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes

et al. 2020

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A palindrome in DNA is like a palindrome in language, but when read backwards, it is a complement of the forward sequence; effectively, the two halves of a sequence complement each other from its midpoint like in a double strand of DNA. Palindromes are distributed throughout the human genome and play significant roles in gene expression and regulation. Palindromic mutations are linked to many human diseases, such as neuronal disorders, mental retardation, and various cancers. In this work, we computed and analyzed the palindromic sequences in the human genome and studied their conservation in personal genomes using 1000 Genomes data. We found that ~30% of the palindromes exhibit variation, some of which are caused by rare variants. The analysis of disease/trait-associated single-nucleotide polymorphisms in palindromic regions showed that disease-associated risk variants are 14 times more likely to be present in palindromic regions than in other regions. The catalog of palindromes in the reference genome and 1000 Genomes is being made available here with details on their variations in each individual genome to serve as a resource for future and retrospective whole-genome studies identifying statistically significant palindrome variations associated with diseases or traits and their roles in disease mechanisms.

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Clustering DNA sequences using the out-of-place measure with reduced n-grams

Huang

2016

Journal of Theoretical Biology

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Suite of Tools for Statistical N-Gram Language Modeling for Pattern Mining in Whole Genome Sequences

Cited by 4 publications

References 47 publications

A pilot study on the prevalence of DNA palindromes in breast cancer genomes

A pilot study on the prevalence of DNA palindromes in breast cancer genomes

A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes

Clustering DNA sequences using the out-of-place measure with reduced n-grams

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