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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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Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD
Sequence alignments are the foundations of life science research, but most innovation so far focuses on optimal alignments, while information derived...
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Optimal Alignment
We change into the chapter directory and make the directory for this chapter, 2. We change into that directory, make the directory for this section,...
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Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data
Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including novel and sample-specific isoforms....
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Optimal Sequence Alignment to ED-Strings
Partial Order Alignment (POA) was introduced by Lee et al. in 2002 to allow the alignment of a string to a graph-like structure representing a set...
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Escape-hatching decisions show adaptive ontogenetic changes in how embryos manage ambiguity in predation risk cues
AbstractAs animals develop, their capacities to sense cues, assess threats, and perform actions change, as do the relative costs and benefits that...
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Sequence Alignment
The sequence analysis is one of the most effective and commonly applied methods (explicity or implicitly) in biological research. Thus, in this...
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MGcount: a total RNA-seq quantification tool to address multi-map** and multi-overlap** alignments ambiguity in non-coding transcripts
BackgroundTotal-RNA sequencing (total-RNA-seq) allows the simultaneous study of both the coding and the non-coding transcriptome. Yet, computational...
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Phylogeny-Aware Alignment with PRANK and PAGAN
Evolutionary analyses require sequence alignments that correctly represent evolutionary homology. Evolutionary homology and proteins’ structural...
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Resolving taxonomic ambiguity and distribution of Tremoctopus gracilis (Cephalopoda: Tremoctopodidae) based on molecular evidence
The octopus of the genus Tremoctopus from the Arabian Sea has not been investigated in the past. This study reports on the rare pelagic octopus Tremoct...
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Twadn: an efficient alignment algorithm based on time war** for pairwise dynamic networks
BackgroundNetwork alignment is an efficient computational framework in the prediction of protein function and phylogenetic relationships in systems...
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An approach for proteins and their encoding genes synonyms integration based on protein ontology
BackgroundBiological research is generating high volumes of data distributed across various sources. The inconsistent naming of proteins and their...
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CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species
BackgroundCircular RNAs (circRNAs) are a class of non-coding RNAs formed by pre-mRNA back-splicing, which are widely expressed in animal/plant cells...
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Cooperation of Spaln and Prrn5 for Construction of Gene-Structure-Aware Multiple Sequence Alignment
Gene-structure-aware multiple sequence alignment (GSA-MSA) is conventionally used as a tool for analyzing evolutionary changes in gene structure,...
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Measuring, visualizing, and diagnosing reference bias with biastools
Many bioinformatics methods seek to reduce reference bias, but no methods exist to comprehensively measure it.
Biastools analyzes and categorizes...
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Alignment- and reference-free phylogenomics with colored de Bruijn graphs
BackgroundThe increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of...
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An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics
BackgroundProteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom...
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The TrEase web service: inferring phylogenetic trees with ease
Phylogenetic inference is done regularly in many biological studies not focussed on the phylogeny itself, but which use phylogeny as a tool to infer...
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Homology Modeling of the G Protein-Coupled Receptors
G protein-coupled receptors (GPCRs) are therapeutically important family of membrane proteins. Despite growing number of experimental structures...