Related papers: Champuru 2: Improved scoring of alignments and a u…
In this paper, we have proposed a novel feature descriptors combining color and texture information collectively. In our proposed color descriptor component, the inter-channel relationship between Hue (H) and Saturation (S) channels in the…
Assessing the correctness of genome assemblies is an important step in any genome project. Several methods exist, but most are computationally intensive and, in some cases, inappropriate. Here I present baa.pl, a fast and easy-to-use…
The two most common data-structures for genome indexing, FM-indices and hash-tables, exhibit a fundamental trade-off between memory footprint and performance. We present Ranger, a new indexing technique for nucleotide sequences that is both…
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…
The importance of the use of networks to model and analyse biological data and the interplay of bio-molecules is widely recognised. Consequently, many algorithms for the analysis and the comparison of networks (such as alignment algorithms)…
Evaluating AMR parsing accuracy involves comparing pairs of AMR graphs. The major evaluation metric, SMATCH (Cai and Knight, 2013), searches for one-to-one mappings between the nodes of two AMRs with a greedy hill-climbing algorithm, which…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…
Composed Image Retrieval (CIR) is a challenging image retrieval paradigm. It aims to retrieve target images from large-scale image databases that are consistent with the modification semantics, based on a multimodal query composed of a…
The ancestral recombination graph (ARG) is the model of choice in statistical genetics to model population ancestries. Software capable of simulating ARGs on a genome scale within a reasonable amount of time are now widely available for…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…
Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs…
Asterias (\url{http://www.asterias.info}) is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI). Most of our applications allow the…
At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the…
Timelapse images of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide rich information on cell structure and contractile function. However, it is challenging to reproducibly generate tissue samples and conduct…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Most existing cross-modal retrieval methods employ two-stream encoders with different architectures for images and texts, \textit{e.g.}, CNN for images and RNN/Transformer for texts. Such discrepancy in architectures may induce different…
Motivation: The pan-genome can be stored as elastic-degenerate (ED) string, a recently introduced compact representation of multiple overlapping sequences. However, a search over the ED string does not indicate which individuals (if any)…
Pathological glomerulus classification plays a key role in the diagnosis of nephropathy. As the difference between different subcategories is subtle, doctors often refer to slides from different staining methods to make decisions. However,…