Related papers: DNA Sequence Alignment by Window based Optical Cor…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently…
The Basic Local Alignment Search Tool (BLAST) is currently the most popular method for searching databases of biological sequences. BLAST compares sequences via similarity defined by a weighted edit distance, which results in it being…
Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…
A basic assumption of molecular biology is that proteins sharing close three-dimensional (3D) structures are likely to share a common function and in most cases derive from a same ancestor. Computing the similarity between two protein…
Bioinformatics, which is now a well known field of study, originated in the context of biological sequence analysis. Recently graphical representation takes place for the research on DNA sequence. Research in biological sequence is mainly…
It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose that the solution is based on a parallelized search implemented by freely…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
Similarity analysis using neural networks has emerged as a powerful technique for understanding and categorizing complex patterns in various domains. By leveraging the latent representations learned by neural networks, data objects such as…
Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous…
We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent…
Real-world data contains various kinds of errors. Before analyzing data, one usually needs to process the raw data. However, traditional data processing based on exactly match often misses lots of valid information. To get high-quality…
This study proposes a deep learning-based approach for discovering loops in programming code according to their potential for parallelization. Two genetic algorithm-based code generators were developed to produce two distinct types of code:…
We propose an optical parallel computation similar to quantum computation that can be realized by introducing pseudorandom phase sequences into classical optical fields with two orthogonal modes. Based on the pseudorandom phase sequences,…
Oligonucleotide arrays are used in a wide range of genomic analyses, such as gene expression profiling, comparative genomic hybridization, chromatin immunoprecipitation, SNP detection, etc. During fabrication, the sites of an…
The massive quantities of genomic data being made available through gene sequencing techniques are enabling breakthroughs in genomic science in many areas such as medical advances in the diagnosis and treatment of diseases. Analyzing this…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…