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Seamlessly integrated with other public EST resources, such as NCBI dbEST [ 11], Trace View [ 15], ORF Finder [ 20], UniGene [ 21] and Gene Indices [ 22], ConiferEST provides the community an invaluable and complementary resource for data validation, visualization and mining of previously ignored sequence features in growing datasets of conifer ESTs.
Indeed, for most Rfam families, the structural information is well below the 20 bits that would be required to push the E-value below 1 in a small, 1M bacterial genome in a structure-based search that completely ignored sequence conservation.
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We ignored sequences without homology with known toxins for all four assemblies.
We ignored sequences without homology with known toxins families and added any resulting unique toxins to our database.
For these analyses, we ignored sequences in which the remnant TE was present in A. thaliana but absent in A. lyrata.
As well we did not use sequences from Chaetognatha, due to their uncertain relation to Lophotrochozoa and we ignored sequences from the molluscs Albinaria, Aplysia, Biomphalaria, which did not cluster with the other molluscs in the first analysis.
As a consequence of ignoring sequence ambiguities, the final (haploid) genome size in units of base pairs (bp) may differ slightly from values commonly reported in the literature.
By ignoring sequence gaps, we minimized the effect of alignment errors or incomplete sequences on our calculations.
As demonstrated above, the organically grown miRBase has lead to substantial risks of miRNA identity confusion and ignoring sequence annotation changes.
As a result, correct interpretation, comparison and integration of miRNA study results are compromised, which we demonstrate here by assessing the impact of ignoring sequence annotation changes.
First, they are both based on a simple parsimony criterion that ignores sequence support for the inferred gene trees, making them prone to over-fitting the gene tree to the species tree topology.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com