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RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms
BackgroundUnderstanding the transcriptome has become an essential step towards the full interpretation of the biological function of a cell, a tissue...
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plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style
BackgroundThe visual sequence logo has been a hot area in the development of bioinformatics tools. ggseqlogo written in R language has been the most...
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Scalable and unbiased sequence-informed embedding of single-cell ATAC-seq data with CellSpace
Standard scATAC sequencing (scATAC-seq) analysis pipelines represent cells as sparse numeric vectors relative to an atlas of peaks or genomic tiles...
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SEDA 2024 update: enhancing the SEquence DAtaset builder for seamless integration into automated data analysis pipelines
BackgroundThe initial version of SEDA assists life science researchers without programming skills with the preparation of DNA and protein sequence...
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Direct prediction of intrinsically disordered protein conformational properties from sequence
Intrinsically disordered regions (IDRs) are ubiquitous across all domains of life and play a range of functional roles. While folded domains are...
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Sequence-Based Nanobody-Antigen Binding Prediction
Nanobodies (Nb) are monomeric heavy-chain fragments derived from heavy-chain only antibodies naturally found in Camelids and Sharks. Their...
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DNA Sequence Assembly and Annotation of Genes
This chapter describes the different sequencing strategies, the pros and cons of the different strategies to help you select the optimal DNA...
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MIxS-SA: a MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms
The symbiont-associated (SA) environmental package is a new extension to the minimum information about any (x) sequence (MIxS) standards, established...
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Functional annotation of a divergent genome using sequence and structure-based similarity
BackgroundMicrosporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high...
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Multiple Sequence Alignment
A multiple sequence alignment (MSA) is an alignment of three or more sequences. Given n strings S1, ... , Sn (...
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Classification of DNA Sequence Based on a Non-gradient Algorithm: Pseudoinverse Learners
This chapter proposes a prototype-based classification approach for analyzing DNA barcodes that uses a spectral representation of DNA sequences and a...
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Semi-supervised learning improves regulatory sequence prediction with unlabeled sequences
MotivationGenome-wide association studies have systematically identified thousands of single nucleotide polymorphisms (SNPs) associated with complex...
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PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins
BackgroundNumerous tools exist for biological sequence comparisons and search. One case of particular interest for immunologists is finding matches...
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Finding identical sequence repeats in multiple protein sequences: An algorithm
In recent years, several experimental evidences suggest that amino acid repeats are closely linked to many disease conditions, as they have a...
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Transgenerational effects of grandparental and parental diets combine with early-life learning to shape adaptive foraging phenotypes in Amblyseius swirskii
Transgenerational effects abound in animals. While a great deal of research has been dedicated to the effects of maternal stressors such as diet...
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EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment
BackgroundAdding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with...
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Mock samples resolve biases in diversity estimates and quantitative interpretation of zooplankton metabarcoding data
Metabarcoding is a rapidly develo** tool in marine zooplankton ecology, although most zooplankton surveys continue to rely on visual identification...
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mtDNAcombine: tools to combine sequences from multiple studies
BackgroundToday an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA...
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Identification of the Sequence and the Length of Telomere DNA
Telomeres are essential nucleoprotein structures at the very ends of linear eukaryote chromosomes. They shelter the terminal genome territories...
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A single cell RNA sequence atlas of the early Drosophila larval eye
The Drosophila eye has been an important model to understand principles of differentiation, proliferation, apoptosis and tissue morphogenesis....
