The proposed algorithm abstracts the target time series into mutually overlapping conceptual granules sequences then predicts them by inference judgment of qualitative concept extension.
Analysis of the conceptual protein sequences is consistent with this idea: The cSmad7a ORF encodes a protein of at least 384 amino acids, while the predicted genomic cSmad7 protein sequence is 222 amino acids long.
Various computational functional annotations were performed on the conceptual protein sequences.
Indeed, the three conceptual polypeptide sequences from these contigs align to a contiguous region of the Disabled protein from T. castaneum, supporting this hypothesis.
Various sequence analyses and manipulations involving sequence alignments, conceptual translation, protein sequence examinations and calculations (e.g. molecular weight, isoelectric point) were carried out with Geneious v5.6 and v6.
To identify contigs coding for sulfur-rich proteins induced in mature seed of SMARC1N-PN1, conceptranslationstiofsequencesences were compared with de novo sequenced peptides from previously obtained liquid chromatography-tandem mass spectrometry (LC-MS/MS) data [ 11].
The conceptual amino acid sequences of these proteins were additionally analyzed using three algorithms (MitoProt, Psort II, and TargetP) which calculate the N-terminal region of a given protein that could support a mitochondrial leader sequence.
The conceptual amino acid sequences of these fragments showed a high degree of similarity with the region of the CcTra protein encoded by exons 2 4, indicating that a fragment of the putative AoTra protein had been isolated.
'PAL2NAL' [ 44] was used to construct codon alignments between protein sequences (conceptual amino acid translation sequences in the case of pseudogenes) and corresponding DNA sequences, separately, for orthologous pseudogenes and parental protein coding genes.
