Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
By Brian J. Haas, Arthur L. Delcher, Stephen M. Mount, Jennifer R. Wortman, R. Smith, L. Hannick, R. Maiti, C. Ronning, D. Rusch, Christopher D. Town and 2 more. Nucleic Acids Research, 2003
2,153 citations recorded by the source corpus.
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.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/d363cfe06fb1428791f29c7825f9ea5e3956af92
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In Molecular Biology
- Mario Stanke
- Mark Borodovsky
- Steven L. Salzberg
- Mark Yandell
- Tomás Bruna
- Katharina Jasmin Hoff
- Daniel Ence
- L. Gabriel
In Plant Science
- A. E. Douglas
- Mario Stanke
- Katharina Jasmin Hoff
- N. Moran
- Georg Jander
- Daniel Ence
- Mark Yandell
- Mihaela Pertea
Citations in the corpus
- The TIGR Rice Genome Annotation Resource: improvements and new features (2006, methodology): “Second, we utilized an improved version of PASA [PASA2, (17)] optimized for the rice genome sequence through manual evaluation of rice gene models.”
- A beginner's guide to eukaryotic genome annotation (2012, methodology): “This is the process used by PASA 56,82 , Gnomon 73 and MAKER 10 .”
- Genome Annotation in Plants and Fungi: EuGene as a Model Platform (2008, methodology): “Cheung from The Institute for Genome Research for providing the FGenesH predictions and PASA-based EST alignments [48] for Medicago truncatula annotation in the framework of the IMGAG consortium.”
- Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments (2007, methodology): “…a retroactive processing of a set of pre-existing gene structure annotations, whereby alignment assemblies are incorporated into untranslated region annotations, exon modifications, correctly splitting or merging predicted gene structures, and used to model alternative splicing isoforms [33].”
- Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “The SEQCLEAN program is part of the PASA pipeline (Haas et al., 2003).”
- Computational methods for transcriptome annotation and quantification using RNA-seq (2011, methodology): “Cufflinks uses an approach originally developed for EST assembly 7 , to connect aligned reads into a graph based on the location of their spliced alignments 29 .”