Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• OPTIC: orthologous and paralogous transcripts in clades.

  PMID 17933761 · PMC2238935 · Nucleic acids research · 2008 · 6 claims · 7 setups

  Full-text index only

  OPTIC is a database providing gene predictions and orthology assignments for three clades: amniotes (human, dog, mouse, opossum, platypus, chicken), 12 Drosophila species, and 4 Caenorhabditis nematodes.

  drosophila translated gene orthologous homology-based all-against-all tree-based

• annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.

  PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups

  Has reproduction · 78

  annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.

  chick real simulated pacbio illumina hybrid

• AceView: a comprehensive cDNA-supported gene and transcripts annotation.

  PMID 16925834 · PMC1810549 · Genome biology · 2006 · 8 claims · 4 setups

  Full-text index only

  At the mRNA level, AceView transcripts are the closest match to Gencode transcripts among all evaluated methods, including alternative splice variants

  genome encode caenorhabditis comparative n-to-n cds