The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
Open accessAbstract
The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all available transcript data and capturing subtle splicing variations. Complete and partial gene structures identified by this method were used to improve The Institute for Genomic Research Arabidopsis genome annotation (TIGR release v.4.0). The alignment assemblies permitted the automated modeling of several novel genes and >1000 alternative splicing variations as well as updates (including UTR annotations) to nearly half of the approximately 27 000 annotated protein coding genes. The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations.
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Cites
Improved tools for biological sequence comparison.
Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
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<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
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Computational discovery of internal micro-exons
Volfovsky, N., Haas, B. J., & Salzberg, S. L. (2003) · Genome Research · doi:10.1101/gr.677503 · Cited by 87
Self-citation
Cited by
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Stanke, M., Diekhans, M., Baertsch, R., & Haussler, D. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn013 · Cited by 2,605
GMAP: A genomic mapping and alignment program for mRNA and EST sequences
Wu, T. D., & Watanabe, C. K. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti310 · Cited by 2,354
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells
Yan, L., Yang, M., Guo, H., Yang, L., Wu, J., Li, R., Liu, P., Lian, Y., Zheng, X., Yan, J., et al. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2660 · Cited by 1,740
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome
Cheng, C., Krishnakumar, V., Chan, A. P., Thibaud‐Nissen, F., Schobel, S., & Town, C. D. (2017) · The Plant Journal · doi:10.1111/tpj.13415 · Cited by 1,317
Metadata
- Authors
- Haas, B. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-10-01
- Volume
- 31
- Issue
- 19
- Pages
- 5654-5666
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2141165178
- Cited by
- 2,296
- References
- 4
- FWCI
- 7.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
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