The strongest sequence differences between the mammalian and the yeast proteins are in the 24 C-terminal amino acids of RPS3A, which show a very poor alignment, with large gaps.
The EMVC method can also be used for the general refinement of gene set collections, either to create versions of a gene set collection that are customized for a specific domain or to identify and entirely remove annotations that exhibit poor alignment with a broad selection of genomic datasets.
In case of Plasmodium falciparum, PF11_0220 (Molecular Function GO 0004672, protein kinase activity, evidence code IDA, source: http://www.plasmodb.org) is a known protein kinase which shows poor alignment with known yeast protein kinase with BLOSUM series of matrices.
After excluding patients with motion artefacts, poor alignment with histology, and benign and nonbreast-originating disease, nine patients were evaluable.
Furthermore, cytoarchitectonic zones, including BAs 44 and 45, have been shown to have poor alignment with macroanatomy in the frontal lobes (e.g., [ 14, 27 29]).
32 Collectively, these results reflect widespread lack of knowledge of gout and poor alignment with current recommendations of best practice within the UK.
The PfSSM (Plasmodium falciparum Specific Substitution Matrices) were developed basically for P. falciparum and particularly for those proteins which do not find their orthologs in other eukaryotes or show very poor alignment with their orthologs.
All hemiascomycetous yeast proteins involved in glucan synthesis or its regulation are 3- to 10-fold longer in sequences, and show very poor alignments with SAKL0H22528p (not shown).
This can be compared to a very poor alignment, for example 'disease – sjuk', which with a frequency of 1 will yield a qvalue of 0.0196 derived from 1/(48+3), given that 'disease' occurs in 48 and 'sjuk' in 3 different candidate term pairs.
Pressey, R. L., Visconti, P. & Ferraro, P. J. Making parks make a difference: poor alignment of policy, planning and management with protected-area impact, and ways forward.
