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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Versatile and open software for comparing large genomes.
PMID 14759262 · PMC395750 · Genome biology · 2004 · 8 claims · 8 setups
MUMmer 3.0 efficiently handles comparisons of large eukaryotic genomes at varying evolutionary distances
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Full-text index only
FeatureScan: revealing property-dependent similarity of nucleotide sequences.
PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups
FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters
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Has reproduction · 99
getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories.
PMID 35804320 · PMC9264741 · BMC bioinformatics · 2022 · 8 claims · 8 setups
getSequenceInfo (gSeqI) allows programmatic (CLI) or GUI-based retrieval of sequence data and metadata from GenBank, RefSeq, and ENA across Linux, MacOS, and Windows.
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Has reproduction · 45
Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.
PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups
Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.