2003
DOI: 10.1093/nar/gkg770
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Abstract: 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 Institut… Show more

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Cited by 1,568 publications
(1,312 citation statements)
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References 44 publications
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“…To produce the current gene set, we used the homology-based FgenesH and GenomeScan predictions. The best gene prediction at each locus was selected and integrated with EST assemblies using the PASA program 37 . The gene set shown in the browser was generated from the input gene models at JGI.…”
Section: Research Article Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…To produce the current gene set, we used the homology-based FgenesH and GenomeScan predictions. The best gene prediction at each locus was selected and integrated with EST assemblies using the PASA program 37 . The gene set shown in the browser was generated from the input gene models at JGI.…”
Section: Research Article Methodsmentioning
confidence: 99%
“…The corresponding genomic regions were extended by 1 kb in each direction and submitted to FgenesH and GenomeScan, along with related angiosperm peptides and/or ORFs from the overlapping EST assemblies. These two sets of predictions were integrated with expressed sequence information using PASA 37 against ,260,000 Eucalyptus EST assemblies. The results were filtered to remove genes identified as transposon-related.…”
Section: Research Article Methodsmentioning
confidence: 99%
“…Repeat sequences were identified in the assembled genome and masked by RepeatMasker, RepeatScout and TransposonPSI, based on known repeat elements in RepBase databases and TIGR Plant Repeat Databases, and the papaya novel repeat database constructed in this study 33,34 . Program to Assemble Spliced Alignments (PASA) 35 was used to generate spliced alignments of papaya unigenes to the unmasked assembly, which was then used in training ab initio gene prediction software Augustus, GlimmerHMM and SNAP [36][37][38] . Ab initio gene prediction software Fgenesh, Genscan and TWINSCAN were trained on Arabidopsis 39-41 .…”
Section: Methodsmentioning
confidence: 99%
“…After removing the adapter sequences, the reads were mapped to the E. pusillum genome using PASA [26] and ORFs were found from the PASA assembly. Augustus [27], GeneID [28], and GeneMark-ES [29] programs were used to predict the gene models for the genome, and then the gene models generated by EVM [30] were updated by PASA.…”
Section: Mapping Assembly Of the Transcriptome And Differential Exprementioning
confidence: 99%