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).
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Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.
PMID 15790396 · PMC1087472 · BMC bioinformatics · 2005 · 8 claims · 7 setups
Paircomp, FamilyRelationsII, and Cartwheel together form an integrated system for comparing, viewing, and managing analyses of BAC-sized (~100 kb) genomic sequence pairs.
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Assessing the gene space in draft genomes.
PMID 19042974 · PMC2615622 · Nucleic acids research · 2009 · 6 claims · 7 setups
The proportion of mapped CEGs in a draft genome assembly is a useful metric for describing gene space completeness, complementing N50 and x-fold coverage.
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Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.
PMID 18307801 · PMC2268679 · BMC genomics · 2008 · 8 claims · 8 setups
eBLAT detects up to 75% more conserved bases than original BLAT alignments, with the largest gains between evolutionarily distant orthologs
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Benchmarking tools for the alignment of functional noncoding DNA.
PMID 14736341 · PMC344529 · BMC bioinformatics · 2004 · 8 claims · 4 setups
Global alignment tools (Avid, ClustalW, Lagan, Needle, DiAlign-G) typically have higher sensitivity over entire noncoding sequences and within constrained blocks than local tools
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Ensembl 2005.
PMID 15608235 · PMC540092 · Nucleic acids research · 2005 · 8 claims · 4 setups
Ensembl's automatic gene build system can flexibly and reliably annotate a wide variety of genomes with limited species-specific evidence.