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If this correlation is significantly negative, if small underpowered studies have larger effect sizes than larger studies, then there is reason to suspect the presence of publication or retrieval bias in the database.
The scoring method uses a random model to limit genome representation bias in the database and avoid assigning taxonomic labels by random chance when a novel organism is not represented in the reference database.
We ascribe this (at least for the two first groups) to a bias in the database registration, resulting in some heifer-rearing herds being included in Group 2, adding to the within-group variation.
Given that the cDNA libraries from which the Lycopersicon ESTs were derived appear to be as varied in tissue/organ type and developmental stage as the other large EST databases analyzed, it appears likely that bias in the database does not completely explain the low numbers of expressed MSTs.
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The apparent predominance of Spy elements in insects could represent a bias in the databases for insect genomes.
Microbial genome projects have introduced a strong bias in the databases toward certain kinds of terrestrial bacteria.
The resulting data set is overrepresented by sequences from insect and vertebrate (especially mammalian) species due to the bias in the databases.
While the seed alignments are claimed to be phylogenetically diverse, constituting representative sequences from different phyla, the large number of sequences that make up the final optimal alignments for each group from NCBI sources may give false impressions of the level of sequence conservation at a given site due to sampling bias in the databases themselves.
Section 6 points out to some possible biases in the database which are needed to be taken into account when interpreting results of evaluation on GUC100.
Given the broad distributions of percent identities, alignment lengths and e-values for alignments of type 1 peptides, it seems reasonable to expect that biases in the databases affect these distributions, further confounding assignments based on alignment alone.
One source of error may be experimental bias in the MINT database.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com