The DOI matches its Crossref record.
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
Open accessAbstract
Summary: We describe two new Generalized Hidden Markov Model implementations for ab initio eukaryotic gene prediction. The C/C++ source code for both is available as open source and is highly reusable due to their modular and extensible architectures. Unlike most of the currently available gene-finders, the programs are re-trainable by the end user. They are also re-configurable and include several types of probabilistic submodels which can be independently combined, such as Maximal Dependence Decomposition trees and interpolated Markov models. Both programs have been used at TIGR for the annotation of the Aspergillus fumigatus and Toxoplasma gondii genomes. Availability: Source code and documentation are available under the open source Artistic License from http://www.tigr.org/software/pirate.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cited by
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172
AUGUSTUS: ab initio prediction of alternative transcripts
Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., & Morgenstern, B. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl200 · Cited by 2,829
The genome of the cucumber,Cucumis sativus L
Huang, S., Li, R., Zhang, Z., Li, L., Gu, X., Fan, W., Lucas, W. J., Wang, X., Xie, B., Ni, P., et al. (2009) · Nature Genetics · doi:10.1038/ng.475 · Cited by 1,490
The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes
Liu, S., Liu, Y., Yang, X., Tong, C., Edwards, D., Parkin, I. A. P., Zhao, M., Ma, J., Yu, J., Huang, S., et al. (2014) · Nature Communications · doi:10.1038/ncomms4930 · Cited by 1,161
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J. H., Senin, P., Wang, W., Ly, B. V., Lewis, K. L. T., et al. (2008) · Nature · doi:10.1038/nature06856 · Cited by 1,084
Self-citation
Metadata
- Authors
- Majoros, W. H., Pertea, M., & Salzberg, S. L.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-05-14
- Volume
- 20
- Issue
- 16
- Pages
- 2878-2879
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2121840477
- Cited by
- 1,934
- References
- 0
- FWCI
- 5.25
- Type
- journal article
- Language
- en
- Open access
- bronze
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. https://app.cochat.ai/papers/10.1093/bioinformatics/bth315
- The paper
- Majoros, W. H., Pertea, M., & Salzberg, S. L. (2004). TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics. https://doi.org/10.1093/bioinformatics/bth315
Data sources
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.
