scholarly journals MFEA: An evolutionary approach for motif finding in DNA sequences

2020 ◽  
Vol 21 ◽  
pp. 100466
Author(s):  
Faisal Bin Ashraf ◽  
Md Shafiur Raihan Shafi
Keyword(s):  
Dna Sequences ◽  
Motif Finding ◽  
Evolutionary Approach

scholarly journals HTS-IBIS: fast and accurate inference of binding site motifs from HT-SELEX data

2015 ◽  
Author(s):  
Yaron Orenstein ◽  
Ron Shamir
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Large Scale ◽  
Motif Finding ◽  
Binding Prediction ◽  
Large Scale Tests ◽  
Automatic Algorithm ◽  
Inference Task

Recent technological advancements enable measuring the binding of a transcription factor to thousands of DNA sequences, in order to infer its binding preferences. High-throughput-SELEX measures protein-DNA binding by deep sequencing over several cycles of enrichment. We devised a new algorithm called HTS-IBIS for the inference task. HTS-IBIS corrects for technological biases, selects the cycle and k, and builds a motif starting from a consensus k-mer in that cycle. In large scale tests, HTS-IBIS outperformed the extant automatic algorithm for the motif finding task on both in vitro and in vivo binding prediction.

EMPLOYING FUZZY C-MEANS FOR DNA TRANSCRIPTION FACTOR BINDING SITE IDENTIFICATION

2010 ◽  
Vol 19 (01) ◽  
pp. 15-30 ◽  
Author(s):  
TURGAY İBRİKCİ ◽  
MUSTAFA KARABULUT
Keyword(s):  
Machine Learning ◽  
Dna Sequences ◽  
Motif Discovery ◽  
Clustering Algorithm ◽  
Motif Finding ◽  
Synthesis Process ◽  
Learning Approach ◽  
Fuzzy C Means ◽  
Dna Motif ◽  
Machine Learning Approach

DNA motif discovery is an important task since it helps to better understand the regulation of the transcription in the protein synthesis process. This paper introduces a novel method for the task of DNA motif finding where the proposed method adopts machine-learning approach by the use of a well-known clustering algorithm, Fuzzy C-Means. The method is explained in detail and tested against DNA sequences extracted from the genome of Saccharomyces cerevisiae and Escherichia coli organisms. Experimental results suggest that the algorithm is efficient in finding statistically interesting features existing in the DNA sequences. The comparison of the algorithm with the well-known motif finding tools, MEME and MDScan, which are built on statistical and word-enumerative models, shows the advantages of the proposed method over the existing tools and the promising direction of the machine-learning approach.

Cognitive gadgets: A provocative but flawed manifesto

2019 ◽  
Vol 42 ◽  
Author(s):  
Marco Del Giudice
Keyword(s):  
Theory Of Mind ◽  
Cultural Differences ◽  
Twin Studies ◽  
Cross Cultural ◽  
Evolutionary Approach ◽  
Genetic Inheritance ◽  
Double Standards ◽  
Cross Cultural Differences ◽  
Cherry Picking ◽  
Dichotomous Thinking

Abstract The argument against innatism at the heart of Cognitive Gadgets is provocative but premature, and is vitiated by dichotomous thinking, interpretive double standards, and evidence cherry-picking. I illustrate my criticism by addressing the heritability of imitation and mindreading, the relevance of twin studies, and the meaning of cross-cultural differences in theory of mind development. Reaching an integrative understanding of genetic inheritance, plasticity, and learning is a formidable task that demands a more nuanced evolutionary approach.

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

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