Related papers: The TAG array of a multiple sequence alignment
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…
For taxonomic classification, we are asked to index the genomes in a phylogenetic tree such that later, given a DNA read, we can quickly choose a small subtree likely to contain the genome from which that read was drawn. Although popular…
Sequence data, such as DNA, RNA, and protein sequences, exhibit intricate, multi-scale structures that pose significant challenges for conventional analysis methods, particularly those relying on alignment or purely statistical…
Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
We introduce a method to reduce constituent parsing to sequence labeling. For each word w_t, it generates a label that encodes: (1) the number of ancestors in the tree that the words w_t and w_{t+1} have in common, and (2) the nonterminal…
Recent generative learning models applied to protein multiple sequence alignment (MSA) datasets include simple and interpretable physics-based Potts covariation models and other machine learning models such as MSA-Transformer (MSA-T). The…
The Burrows-Wheeler Transform (BWT) of a string is an invertible permutation of the string, which can be used for data compression and compact indexes for string pattern matching. Ganguly et al. [SODA, 2017] introduced the parameterized BWT…
In recent years, the focus of bioinformatics research has moved from individual sequences to collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform (BWT) in string processing, a number of dedicated tools have…
Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…
Evolutionary modeling applications are the best way to provide full information to support in-depth understanding of evaluation of organisms. These applications mainly depend on identifying the evolutionary history of existing organisms and…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
In sequence-based predictions, conventionally an input sequence is represented by a multiple sequence alignment (MSA) or a representation derived from MSA, such as a position-specific scoring matrix. Recently, inspired by the development in…
Introduced about thirty years ago in the field of Data Compression, the Burrows-Wheeler Transform (BWT) is a string transformation that, besides being a booster of the performance of memoryless compressors, plays a fundamental role in the…
We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
The Burrows-Wheeler Transform is a string transformation that plays a fundamental role for the design of self-indexing compressed data structures. Over the years, researchers have successfully extended this transformation outside the…
Multiple Sequences Alignment (MSA) of biological sequences is a fundamental problem in computational biology due to its critical significance in wide ranging applications including haplotype reconstruction, sequence homology, phylogenetic…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…