NCBI Genome Workbench: Desktop Software for Comparative Genomics, Visualization, and GenBank Data Submission
Abstract
The book chapter introduces the National Center for Biotechnology Information (NCBI) Genome Workbench, a desktop GUI software package to manipulate and visualize complex molecular biology models provided in many data formats. Genome Workbench integrates graphical views and computational tools in a single package to facilitate discoveries. In this chapter we provide a step-by-step protocol guidance on how to do comparative analysis of sequences using NCBI BLAST and multiple sequence alignment algorithms, build phylogenetic trees, and use graphical views for sequences, alignments, and trees to validate the findings. The software package can be used to prepare high-quality whole genome submissions to NCBI. The software package is user-friendly and includes validation and editing tools to fix errors as part of preparing the submission.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
BLAST's hashing-based search mechanism is efficient in identifying homologous sequences across species, aiding in the annotation of novel genomes and the discovery of evolutionary conserved regions.
“BLAST's hashing-based search mechanism is efficient in identifying homologous sequences across species, aiding in the annotation of novel genomes and the discovery of evolutionary conserved regions [56].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [56]
Cites
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Whole-Genome Alignment: Methods, Challenges, and Future Directions
Saada, B., Zhang, T., Siga, E., Zhang, J., & Magalhães Muniz, M. M. (2024) · Applied Sciences · doi:10.3390/app14114837 · Cited by 15 · see citing works
- Authors
- Kuznetsov, A., & Bollin, C. J.
- Affiliations
- National Center for Biotechnology Information (US)
- Corresponding author
- Kuznetsov, Anatoliy
- Venue
- Methods in Molecular Biology
- Publisher
- Springer US
- Published
- 2020-12-09
- Volume
- 2231
- Pages
- 261-295
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W3113129282
- Cited by
- 80
- References
- 1
- Citations by year
- 2026: 6 · 2025: 10 · 2024: 19 · 2023: 19 · 2022: 17 · 2021: 8 · 2020: 1
- FWCI
- 15.32
- Type
- book chapter
- Language
- en
- Open access
- closed
- Locations
- Methods in molecular biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
- Keywords
- comparative genomics, sequence visualization, NCBI BLAST, multiple sequence alignment, phylogenetic tree construction, desktop application
- MeSH terms
- Algorithms, Phylogeny, Software, Sequence Alignment, Genome, Computational Biology, Genomics, Databases, Nucleic Acid, PubMed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
