Clustal Omega for making accurate alignments of many protein sequences
Explore this paper's citation graph
Summary
Some recent additions to Clustal Omega are described and some alternative ways of making alignments are benchmarked based on protein structure comparisons or predictions and include a recently described method based on secondary structure prediction.
- Type
- article
- Published
- 2018-01-01
- Cited by
- 1,882
- References
- 23
- Access
- Open access
- OpenAlex
- https://openalex.org/W2750791471
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:10913424
Keywords
Executable, Multiple sequence alignment, Computer science, Benchmark (surveying), Sequence alignment
References
- Evolution of 5S RNA and the non-randomness of base replacement.
- HOMSTRAD: A database of protein structure alignments for homologous families
- Systematic exploration of guide-tree topology effects for small protein alignments
- JPred4: a protein secondary structure prediction server
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- Simple chained guide trees give high-quality protein multiple sequence alignments
- The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
- MAFFT version 5: improvement in accuracy of multiple sequence alignment
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
- Sequence embedding for fast construction of guide trees for multiple sequence alignment
- A benchmark of multiple sequence alignment programs upon structural RNAs
- Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
- MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
- MUSCLE: multiple sequence alignment with high accuracy and high throughput.
- HMMER web server: interactive sequence similarity searching
- BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
- A comprehensive comparison of multiple sequence alignment programs
- T-Coffee: A novel method for fast and accurate multiple sequence alignment.
- Protein homology detection by HMM?CHMM comparison
- CLUSTAL V: improved software for multiple sequence alignment
Cited by
- Cross-Chemistry Leads to Product Diversity from Atromentin Synthetases in Aspergilli from Section Nigri.
- Epitope-based peptide vaccine design and elucidation of novel compounds against 3C like protein of SARS-CoV-2
- Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services
- Predicting Antimicrobial and Other Cysteine-Rich Peptides in 1267 Plant Transcriptomes
- Partially Local Multi-way Alignments
- GH57 amylopullulanase from Desulfurococcus amylolyticus JCM 9188 can make highly branched cyclodextrin via its transglycosylation activity.
- The solution structure of monomeric CCL5 in complex with a doubly-sulfated N-terminal segment of CCR5
- Parallel Evolution of Key Genomic Features and Cellular Bioenergetics Across the Marine Radiation of a Bacterial Phylum
- Redefinition and Unification of the SXT/R391 Family of Integrative and Conjugative Elements
- NS3 from Hepatitis C Virus Strain JFH-1 Is an Unusually Robust Helicase That Is Primed To Bind and Unwind Viral RNA
- Alternative utrophin mRNAs contribute to phenotypic differences between dystrophin‐deficient mice and Duchenne muscular dystrophy
- No wisdom in the crowd: genome annotation in the era of big data – current status and future prospects
- The role of extended Fe4S4 cluster ligands in mediating sulfite reductase hemoprotein activity.
- Functional Evaluation of the π-Helix in the NAD(P)H:FMN Reductase of the Alkanesulfonate Monooxygenase System.
- Thermostability and Specific-Activity Enhancement of an Arginine Deiminase from Enterococcus faecalis SK23.001 via Semirational Design for l-Citrulline Production.
- Thermostable alpha-glucan phosphorylases: characteristics and industrial applications
- Transcriptome and Comparative Genomics Analyses Reveal New Functional Insights on Key Determinants of Pathogenesis and Interbacterial Competition in Pectobacterium and Dickeya spp
- Structure of the GH9 glucosidase/glucosaminidase from Vibrio cholerae
- Structural Prediction of the Dimeric Form of the Mammalian Translocator Membrane Protein TSPO: A Key Target for Brain Diagnostics
- A new statistic for efficient detection of repetitive sequences
Related papers
- Alignment of protein sequences by their profiles
- Homology-extended sequence alignment
- Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
- INTERALIGN: interactive alignment editor for distantly related protein sequences
- ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approach
- ALIGN_MTX - An optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment
- Grammar-based distance in progressive multiple sequence alignment
- Protein Threading Based on Multiple Protein Structure Alignment.