The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
GeSeq – versatile and accurate annotation of organelle genomes
Open accessAbstract
We have developed the web application GeSeq (https://chlorobox.mpimp-golm.mpg.de/geseq.html) for the rapid and accurate annotation of organellar genome sequences, in particular chloroplast genomes. In contrast to existing tools, GeSeq combines batch processing with a fully customizable reference sequence selection of organellar genome records from NCBI and/or references uploaded by the user. For the annotation of chloroplast genomes, the application additionally provides an integrated database of manually curated reference sequences. GeSeq identifies genes or other feature-encoding regions by BLAT-based homology searches and additionally, by profile HMM searches for protein and rRNA coding genes and two de novo predictors for tRNA genes. These unique features enable the user to conveniently compare the annotations of different state-of-the-art methods, thus supporting high-quality annotations. The main output of GeSeq is a GenBank file that usually requires only little curation and is instantly visualized by OGDRAW. GeSeq also offers a variety of optional additional outputs that facilitate downstream analyzes, for example comparative genomic or phylogenetic studies.
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Citations
Cites
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Cited by
CPGAVAS2, an integrated plastome sequence annotator and analyzer
Shi, L., Chen, H., Jiang, M., Wang, L., Wu, X., Huang, L., & Liu, C. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz345 · Cited by 1,249
Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes
Zheng, S., Poczai, P., Hyvönen, J., Tang, J., & Amiryousefi, A. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.576124 · Cited by 382
Cecchin, M., Marcolungo, L., Rossato, M., Girolomoni, L., Cosentino, E., Cuine, S., Li‐Beisson, Y., Delledonne, M., & Ballottari, M. (2019) · The Plant Journal · doi:10.1111/tpj.14508 · Cited by 83
Adaptive evolution of the enigmatic Takakia now facing climate change in Tibet
Hu, R., Li, X., Hu, Y., Zhang, R., Lv, Q., Zhang, M., Sheng, X., Zhao, F., Chen, Z., Ding, Y., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.003 · Cited by 55
Calhoun, S., Bell, T. A. S., Dahlin, L. R., Kunde, Y., LaButti, K., Louie, K. B., Kuftin, A., Treen, D., Dilworth, D., Mihaltcheva, S., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-01859-y · Cited by 60
Metadata
- Authors
- Tillich, M., Lehwark, P., Pellizzer, T., Ulbricht-Jones, E. S., Fischer, A., Bock, R., & Greiner, S.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-05-09
- Volume
- 45
- Issue
- W1
- Pages
- W6-W11
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2612261225
- Cited by
- 3,454
- References
- 1
- FWCI
- 58.62
- Type
- journal article
- Language
- en
- Open access
- gold
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- Tillich, M., Lehwark, P., Pellizzer, T., Ulbricht-Jones, E. S., Fischer, A., Bock, R., & Greiner, S. (2017). GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx391
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