A5039921905- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Advanced Proteomics Techniques and Applications
- Glycosylation and Glycoproteins Research
- RNA Research and Splicing
- RNA modifications and cancer
- Muscle Physiology and Disorders
- Biomedical Text Mining and Ontologies
- Protein Structure and Dynamics
- Gastrointestinal motility and disorders
- Gene expression and cancer classification
- Scientific Computing and Data Management
- Cardiomyopathy and Myosin Studies
- Bacteriophages and microbial interactions
- Cellular transport and secretion
- Genomics and Rare Diseases
- Microbial Metabolic Engineering and Bioproduction
- Algorithms and Data Compression
- Genomics and Chromatin Dynamics
- Enzyme Structure and Function
- Acute Myeloid Leukemia Research
- Nuclear Structure and Function
Laboratoire des Sciences de l'Ingénieur, de l'Informatique et de l'Imagerie
2014-2025
Loughborough University
2022-2025
University Hospitals of Leicester NHS Trust
2022-2025
Université de Strasbourg
2014-2024
Burman University
2021-2023
Duke University
2018-2022
Florida Hospital Medical Group
2022
Cabarrus College of Health Sciences
2022
Radiology Associates
2022
Duke University Hospital
2022
The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for divergent protein sequences. Firstly, individual weights are assigned to each in a partial order downweight near-duplicate sequences and up-weight most ones. Secondly, amino acid substitution matrices varied at different stages according divergence be aligned. Thirdly, residue-specific gap penalties locally reduced hydrophilic regions encourage new gaps potential loop rather than...
CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program W. The system easy to use, providing an integrated performing and profile alignments analysing results. displays in window on screen. A versatile colouring scheme allows user highlight conserved features alignment. Pull-down menus provide all options required traditional New include: ability cut-and-paste sequences change order of alignment, selection subset be realigned, sub-range...
Abstract Summary: The Clustal W and X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of algorithms future has allowed proper porting to latest versions Linux, Macintosh Windows operating systems. Availability: can be run on-line from EBI web server: http://www.ebi.ac.uk/tools/clustalw2. source code executables for Windows, Linux computers are available ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/ Contact:...
The Clustal programs are widely used for carrying out automatic multiple alignment of nucleotide or amino acid sequences. most familiar version is ClustalW, which uses a simple text menu system that portable to more less all computer systems. ClustalX features graphical user interface and some powerful utilities aiding the interpretation alignments preferred interactive usage. Users may run remotely from several sites using Web be downloaded locally on PCs, Macintosh, Unix computers....
In recent years improvements to existing programs and the introduction of new iterative algorithms have changed state-of-the-art in protein sequence alignment. This paper presents first systematic study most commonly used alignment using BAliBASE benchmark alignments as test cases. Even below 'twilight zone' at 10–20% residue identity, best were capable correctly aligning on average 47% residues. We show that often offer improved accuracy though expense computation time. A notable exception...
BAliBASE is a database of manually refined multiple sequence alignments categorized by core blocks conservation length, similarity, and the presence insertions N/C-terminal extensions.From http://www-igbmc. u-strasbg.fr/BioInfo/BAliBASE/index.html
Abstract Multiple sequence alignment is one of the cornerstones modern molecular biology. It used to identify conserved motifs, determine protein domains, in 2D/3D structure prediction by homology and evolutionary studies. Recently, high‐throughput technologies such as genome sequencing structural proteomics have lead an explosion amount information available. In response, several new multiple methods been developed that improve both efficiency quality alignments. Consequently, benchmarks...
Multiple comparison or alignmentof protein sequences has become a fundamental tool in many different domains modern molecular biology, from evolutionary studies to prediction of 2D/3D structure, function and inter-molecular interactions etc. By placing the sequence framework overall family, multiple alignments can be used identify conserved features highlight differences specificities. In this paper, we describe comprehensive evaluation most popular methods for alignment (MSA), based on new...
Abstract Background The Covid19 infection is caused by the SARS-CoV-2 virus, a novel member of coronavirus (CoV) family. CoV genomes code for ORF1a / ORF1ab polyprotein and four structural proteins widely studied as major drug targets. also contain variable number open reading frames (ORFs) coding accessory that are not essential virus replication, but appear to have role in pathogenesis. been less well characterized difficult predict classical bioinformatics methods. Methods We propose...
Position-specific substitution matrices, known as profiles, derived from multiple sequence alignments are currently used to search databases for distantly related members of protein families. The performance the database searches is enhanced by using (i) a weighting scheme which assigns higher weights more sequences based on branch lengths phylogenetic trees, (ii) exclusion positions with mainly padding characters at sites insertions or deletions and (iii) BLOSUM62 residue comparison matrix....
New findings are presented for the ~ 50 residue KH motif, a domain recently discovered in RNA‐binding proteins. The conserved sequence is 10 residues larger than previously reported. Profile searches have revealed new members of this family, including two, E. coli NusA and human GAP‐associated p62 phosphoprotein, which data exists. A nus homolog was detected RNA polymerase gene complex six archaebacterial species may encode an antiterminator. All KH‐containing proteins linked with motif most...
Abstract Background The draft genome assemblies produced by new sequencing technologies present important challenges for automatic gene prediction pipelines, leading to less accurate models. New benchmark methods are needed evaluate the accuracy of in face incomplete assemblies, low coverage and quality, complex structures, or a lack suitable sequences evidence-based annotations. Results We describe construction benchmark, called G3PO (benchmark Gene Protein Prediction PrOgrams), designed...
DbClustal addresses the important problem of automatic multiple alignment top scoring full-length sequences detected by a database homology search. By combining advantages both local and global algorithms into single system, is able to provide accurate alignments highly divergent, complex sequence sets. Local information incorporated ClustalW in form list anchor points between pairs sequences. The method demonstrated using anchors supplied Blast post-processing program, Ballast. rapidity...
DNA translation frames can be disrupted for several reasons, including: (i) errors in sequence determination; (ii) RNA processing, such as intron removal and guide editing; (iii) less commonly, polymerase frameshifting during transcription or ribosomal translation. Frameshifts frequently confound computational activities involving homologous sequences, database searches inferences on structure, function phylogeny made from multiple alignments. A dynamic alignment algorithm is reported here...
Most multiple sequence alignment programs use heuristics that sometimes introduce errors into the alignment. The most commonly used methods to correct these iterative techniques maximize an objective function. We present here alternative, knowledge-based approach combines a number of recently developed two-step refinement process. is divided horizontally and vertically form 'lattice' in which well aligned regions can be differentiated. Alignment correction then restricted less reliable...