Related papers: AliBI: An Alignment-Based Index for Genomic Datase…
Index structures are a building block of query processing and computer science in general. Since the dawn of computer technology there have been index structures. And since then, a myriad of index structures are being invented and published…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Advances in data collecting technologies in genomics have significantly increased the need for tools designed to study the genetic basis of many diseases. Effective statistical methods should excel in both prediction accuracy and biomarker…
Huge DBMSs storing genomic information are being created and engineerized for doing large-scale, comprehensive and in-depth analysis of human beings and their diseases. However, recent regulations like the GDPR require that sensitive data…
Advances in gene sequencing have enabled in silico analyses of microbial genomes and have led to the revision of concepts of microbial taxonomy and evolution. We explore deficiencies in existing multiple sequence global alignment algorithms…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
Background: Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. All existing alignment algorithms rely on heuristic scoring schemes based on biological expertise.…
Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…
Motivation: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and…
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this…
Rapid advancements in technology have led to an increased use of artificial intelligence (AI) technologies in medicine and bioinformatics research. In anticipation of this, the National Institutes of Health (NIH) assembled the Bridge to…
We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment itself can be efficiently viewed with reference to any genome…
Sequence alignment is a fundamental process in computational biology which identifies regions of similarity in biological sequences. With the exponential growth in the volume of data in bioinformatics databases, the time, processing power,…
FM-indexes are a crucial data structure in DNA alignment, for example, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer observed in 2007 that word-based indexes often…
Aligning the entire genome of an organism is a compute-intensive task. Pre-alignment filters substantially reduce computation complexity by filtering potential alignment locations. The base-count filter successfully removes over 68% of the…
Adaptive indexing is a concept that considers index creation in databases as a by-product of query processing; as opposed to traditional full index creation where the indexing effort is performed up front before answering any queries.…
There now exist compact indexes that can efficiently list all the occurrences of a pattern in a dataset consisting of thousands of genomes, or even all the occurrences of all the pattern's maximal exact matches (MEMs) with respect to the…
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…
Large language models (LLMs) are increasingly being used as decision aids. However, users have diverse values and preferences that can affect their decision-making, which requires novel methods for LLM alignment and personalization.…