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"It was disturbing to me that Matt's name was innocently yielding search returns in the ADL database despite having absolutely nothing to do with the co-opting of Pepe by racist assholes," Reynolds said.
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Clusters yielding CM search hits with an E-value of E<10−5 were considered as known, others as novel.
Results from human, fly, and worm are combined at the Animal node in the tree, yielding a search ordering specific to those three multicellular organisms.
Results from fly and worm are combined at the Ecdysozoa node of the tree, yielding a search ordering specific to those two molting organisms.
The MSGR is run on the six organisms individually, yielding independent search orderings for each organism having at least the minimum number of genes orthologous to those genes in the query (five by default).
The key search term utilised was 'social network' for the initial search yielding 14 607 articles.
From an initial search yielding 1444 articles, 22 articles met the criteria for inclusion.
30 Bounding A above zero conveniently eliminates the need to worry about negative match probabilities (P) yielding a valid search probability.
Three of the 31 were eliminated as duplicates to the PubMed search, yielding 28 that were added to the PubMed results for further examination.
As mentioned previously, because the training and testing sets were identical in our case, or close to identical in the Burset and Guigó study [14, 16], we consider the ALLSEQ results as a brute force parameter search yielding what to expect in the ideal case and not necessarily a valid test of prediction performance.
For each Crocodilia, around 90,000 potential exons were retrieved and almost all of them (99.7 99.8) were assembled against a Gallus or a Pelodiscus coding cDNA after a BLASTn search, yielding more than 17,000 consensus sequences.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com