We are analyzing https://link.springer.com/article/10.1186/1741-7007-3-7.

Title:
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release | BMC Biology
Description:
Background Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications. Results Over the course of three years, TIGR has completed its effort to standardize the structural and functional annotation of the Arabidopsis genome. Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories. We present an overview of the methods employed, tools developed, and protocols followed, summarizing the contents of each data release with special emphasis on our final annotation release (version 5). Conclusion Over the entire period, several thousand new genes and pseudogenes were added to the annotation. Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified using Gene Ontology terms.
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Keywords {🔍}

gene, pubmed, genome, annotation, arabidopsis, genes, article, google, scholar, protein, cas, sequence, proteins, sequences, families, central, regions, splicing, plant, alignments, release, data, annotations, database, family, methods, structures, domain, structure, alternative, effort, transcripts, reannotation, functional, bac, chromosome, transcript, including, annotated, size, evidence, analysis, res, bacs, domains, results, biol, function, tigr, ontology,

Topics {✒️}

org/pub/data/a_thaliana/ath1/data_release_supplement/genes_matching_fl_cdnas_not_incorporated org/pub/data/a_thaliana/ath1/data_release_supplement/genes_and_antisense_transcripts org/pub/data/a_thaliana/ath1/data_release_supplement/polycistronictranscripts org/pub/data/a_thaliana/ath1/data_release_supplement/paralogousfamilies org/pub/data/a_thaliana/ath1/data_release_supplement/ath1_r5_go_gene_associations org/pub/software/blast-synteny-toolkit/arabdups_n_xyplotter org/tdb/e2k1/ath1/tandemdups/tandemgenes org/tdb/e2k1/ath1/arabidopsis_genome_duplication org/pub/data/transposableelements/transposon_db org/tigr-scripts/e2k1/arab_gene_phys_ev_classification org/tigr-scripts/euk_manatee/listchromosomes article download pdf gov/geo/query/acc putative udp-glucose 4-epimerase intron-exon boundary refinements putative rna-binding protein single-linkage clustering method older large-scale duplications formamidopyrimidine-dna glycosylase produced resolving intron/exon boundaries fully sequenced/assembled versions c3hc4-type ring finger peer-reviewed publications including article published online eukaryotic genome control van de peer transposon-related sequences consisted gene ontology consortium domain-based classification scheme signature-recognition methods data structure called thaliana-specific domain alignments de la cruz arabidopsis protein-coding genes gene ontology categories vertical marker line domain-based protein classification gene-prediction programs gene prediction programs gene ontology annotation altered orf yielding controlled vocabularies describing rna-binding specificity gene ontology assignments dna-binding family protein additional sequence-based methods single linkage clustering position-specific gap penalties org/pub/ open reading frames

Questions {❓}

Doolittle RF: Similar amino acid sequences: chance or common ancestry?
How complete a representation of the genome is the version 5 tiling path and pseudomolecules?
Saurin AJ, Borden KL, Boddy MN, Freemont PS: Does this have a familiar RING?
Vanhee-Brossollet C, Vaquero C: Do natural antisense transcripts make sense in eukaryotes?

Schema {🗺️}

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         description:Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications. Over the course of three years, TIGR has completed its effort to standardize the structural and functional annotation of the Arabidopsis genome. Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories. We present an overview of the methods employed, tools developed, and protocols followed, summarizing the contents of each data release with special emphasis on our final annotation release (version 5). Over the entire period, several thousand new genes and pseudogenes were added to the annotation. Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified using Gene Ontology terms.
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         Antisense Transcript
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         Tiling Path
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         general
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      name:The Institute for Genomic Research, Rockville, USA
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      name:The Institute for Genomic Research, Rockville, USA
      name:The Institute for Genomic Research, Rockville, USA
      name:The Institute for Genomic Research, Rockville, USA
      name:The Institute for Genomic Research, Rockville, USA
      name:The Institute for Genomic Research, Rockville, USA
      name:The Institute for Genomic Research, Rockville, USA
      name:The Institute for Genomic Research, Rockville, USA
      name:The Institute for Genomic Research, Rockville, USA

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