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Genes less than 2.5 kb were removed to avoid the spurious identification of smaller blanketed genes.
To the extent that is possible when working with non-model microscopic endoparasites and currently available public data, this approach eliminates spurious identification of contaminant transcripts as being parasite-derived, such as the identification of bryozoan Hox genes as myxozoan [ 9], and thereby enables functional genetic searching beyond taxonomically restricted genes.
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By removing physical interaction data from the process of identifying genetically compensatory pathways, there was also a greater potential for spurious identifications (discussed later).
A straightforward approach to the treatment of protein identifications attributed to single peptide hits allowed the retention of potentially important low abundance identifications (validated by a cross-sample match and de novo interpretation of relevant spectra) while still eliminating potentially spurious identifications (global single peptide hits with no cross-sample match).
This involved the elimination of ~ 500 spurious ORFs, identification of 43 additional small ORFs (50 99 codons), refinement of initiation and termination codons and the identification of new introns.
They also show that high quality (genomic) sequence information for these organisms provides a significant advantage if one wants to achieve greater proteome coverage and lower numbers of spurious protein identifications.
Including these comparisons in the analysis results in the annotation of significantly fewer short ORFs as potentially functional genes; many of those not included in the present analysis were previously suspected to be spurious gene identifications and not functional genes [ 57].
First, we want to compare the performance in identification of spurious PPI using our method with that of MDS-method.
In this experiment, we demonstrate the performance of GGA-method in prediction of missing PPI and identification of spurious PPI in the noisy network.
This fact could, of course, simply point to the identification of spurious targets of selection.
However, as illustrated in this study, small population size may lead to false positives and the identification of spurious SDRs.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com