The DOI matches its Crossref record; 20 of the 20 references it cites were found in a registry or an index; none of the 13 sources its claims cite is checked for support yet.
Alignment of Biological Sequences with Jalview
Open accessAbstract
In this chapter, we introduce core functionality of the Jalview interactive platform for the creation, analysis, and publication of multiple sequence alignments. A workflow is described based on Jalview’s core functions: from data import to figure generation, including import of alignment reliability scores from T-Coffee and use of Jalview from the command line. The accompanying notes provide background information on the underlying methods and discuss additional options for working with Jalview to perform multiple sequence alignment, functional site analysis, and publication of alignments on the web.
Overview
CoChat Summary
TL;DR
This methods chapter presents a step-by-step Jalview workflow for importing, aligning, analyzing, and publishing multiple sequence alignments, including T-Coffee TCS reliability scoring and command-line figure generation. It is a practical protocol rather than an empirical study, and it reports operational limits such as public web-service caps of 1000 sequences × 1000 residues.
Key findings
- Describes Jalview 2.11 functionality for MSA creation, visualization, analysis, and publication, available as a native app, executable JAR, JalviewJS web application, and via Homebrew/BioConda.
- Public alignment services from the University of Dundee are suitable for up to 1000 sequences of at most 1000 residues each, with jobs allowed to run for up to 1 h; larger alignments require a local JABAWS instance or external alignment followed by import.
- Jalview automatically requests up to 90% of physical memory, with a minimum recommended physical memory of 1 GB; there is currently no support for alignments too big to load into memory.
- The chapter details integration with T-Coffee TCS reliability scores, AACon’s 17 additional conservation scores, tree-based grouping, sequence logos, and export to PNG, SVG, EPS, HTML, and BioJS-msaviewer formats.
Methods
- Design: a methods/protocol chapter, not an empirical study; it provides a step-by-step workflow from data import to figure generation.
- Data or sample: no experimental sample is analyzed; Jalview loads an example alignment, tree, and 3D structure on startup, and the command-line example opens `uniref50.fa` and generates `example_fig.png`.
- Main analysis: instructions cover importing sequences/CDS, running MSA web services, evaluating alignment reliability with T-Coffee TCS/M-COFFEE, filtering by occupancy or TCS, coloring and grouping by conservation/trees, and exporting figures interactively or in batch mode.
Limitations
- Stated in the paper: no support is provided for alignments too big to load into memory; Jalview must remain running for the duration of a web-service alignment; in version 2.11 there is no way to reconnect to completed or in-progress web-service jobs, and projects do not preserve web-service job information.
- Stated in the paper: public Dundee services do not permit alignments of greater than 1000 sequences with up to 1000 amino acids each; larger alignments require local JABAWS or external alignment and reimport, which can lose sequence metadata, CDS relationships, features, and hidden columns, and may fail due to sequence-name constraints.
- Stated and evident from the text: figure export has no “Undo” functionality; interactive HTML/BioJS exports may look and behave differently from the Desktop or JalviewJS visualizations; as a methods chapter, it reports no benchmarking or validation of Jalview’s accuracy or performance.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
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Claims the paper makes
0 Valid · 22 Not valid · 11 Not checked · 62 Own results and interpretations
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“As a consequence, global statistics such as consensus and conservation are not always sufficient to identify regions of alignments that are important for the structure and function of a sequence family.”
§ Alignment of Biological Sequences with Jalview > Notes
plainstates a cause- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on 3 assumptions not shown here.
13 references still to check
A free account verifies the references that are still open.
- Probably not a substantial claim. 93
- It may state two separate claims as one. 32
Citations
Cites
Comparative Protein Modelling by Satisfaction of Spatial Restraints
Šali, A., & Blundell, T. L. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1626 · Cited by 12,977
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M., & Barton, G. J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp033 · Cited by 10,235
Self-citationAmino acid substitution matrices from protein blocks.
Henikoff, S., & Henikoff, J. G. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.22.10915 · Cited by 6,218
Sequence logos: a new way to display consensus sequences
Schneider, T. D., & Stephens, R. M. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.20.6097 · Cited by 3,378
Bioconda: sustainable and comprehensive software distribution for the life sciences
The Bioconda Team, Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., & Köster, J. (2018) · Nature Methods · doi:10.1038/s41592-018-0046-7 · Cited by 1,641
An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families
Lichtarge, O., Bourne, H. R., & Cohen, F. E. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0167 · Cited by 1,195
Sussman, J. L., Lin, D., Jiang, J., Manning, N. O., Prilusky, J., Ritter, O., & Abola, E. E. (1998) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444998009378 · Cited by 740
M-Coffee: combining multiple sequence alignment methods with T-Coffee
Wallace, I. M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl091 · Cited by 581
Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation
Livingstone, C. D., & Barton, G. J. (1993) · Bioinformatics · doi:10.1093/bioinformatics/9.6.745 · Cited by 550
Self-citationZvelebil, M. J., Barton, G. J., Taylor, W. R., & Sternberg, M. J. E. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90501-8 · Cited by 435
Self-citation
Cited by
3D cell cultures toward quantitative high-throughput drug screening
Wang, Y., & Jeon, H. (2022) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2022.03.014 · Cited by 147
Oberg, N., Precord, T. W., Mitchell, D. A., & Gerlt, J. A. (2021) · ACS Bio & Med Chem Au · doi:10.1021/acsbiomedchemau.1c00048 · Cited by 127
Somatic mutation and selection at population scale
Lawson, A. R. J., Abascal, F., Nicola, P. A., Lensing, S. V., Roberts, A. L., Kalantzis, G., Baez‐Ortega, A., Brzozowska, N., Moustafa, J. S. E.-S., Vaitkute, D., et al. (2025) · Nature · doi:10.1038/s41586-025-09584-w · Cited by 92
Shaheen, A., Tariq, A., Iqbal, M., Mirza, O., Haque, A., Walz, T., & Rahman, M. (2021) · Antibiotics · doi:10.3390/antibiotics10121455 · Cited by 66
Maintenance of genome sequence integrity in long- and short-lived rodent species
Zhang, L., Dong, X., Tian, X., Lee, M., Ablaeva, J., Firsanov, D., Lee, S.-G., Maslov, A. Y., Gladyshev, V. N., Seluanov, A., et al. (2021) · Science Advances · doi:10.1126/sciadv.abj3284 · Cited by 54
Metadata
- Authors
- Procter, J. B., Carstairs, G. M., Soares, B., Mourão, K., Ofoegbu, T. C., Barton, D., Lui, L., Menard, A., Sherstnev, N., Roldan-Martinez, D., Duce, S., Martin, D. M. A., & Barton, G. J.
- Affiliations
- University of Dundee (GB)
- Université Paris-Sud (FR)
- Capgemini (France) (FR)
- Corresponding author
- Procter, James B.
- ORCID
- Venue
- Methods in Molecular Biology
- Publisher
- Springer US
- Published
- 2020-12-09
- Volume
- 2231
- Pages
- 203-224
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- PMC
- PMC7116599
- OpenAlex
- W3111109655
- Semantic Scholar
- b3d7147bcb4686526c29ed83668b282f7862352b
- Cited by
- 221
- References
- 20
- Citations by year
- 2026: 55 · 2025: 57 · 2024: 35 · 2023: 27 · 2022: 34 · 2021: 13
- FWCI
- 22.94
- Type
- book chapter
- Language
- en
- Update notices
- correction (2021-03-12)
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- www.springer.com/tdm (tdm)
- www.springer.com/tdm (vor)
- Locations
- Methods in molecular biology (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- University of Dundee
- Wellcome Trust (101651/Z/13/Z)
- Scottish Funding Council
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council (BB/L010742/1, BB/R014752/1, BB/L020742/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Keywords
- Jalview, multiple sequence alignment, T-Coffee
- MeSH terms
- Internet Use, Phylogeny, Software, Reproducibility of Results, Sequence Alignment, Sequence Analysis, DNA, Sequence Analysis, Protein, Workflow
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- CoChat. (2026). Citation check: Alignment of Biological Sequences with Jalview. https://app.cochat.ai/papers/10.1007/978-1-0716-1036-7_13
- The paper
- Procter, J. B., Carstairs, G. M., Soares, B., Mourão, K., Ofoegbu, T. C., Barton, D., Lui, L., Menard, A., Sherstnev, N., Roldan-Martinez, D., Duce, S., Martin, D. M. A., & Barton, G. J. (2021). Alignment of Biological Sequences with Jalview. Methods in Molecular Biology. https://doi.org/10.1007/978-1-0716-1036-7_13
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
