Idiom networks for short constituent sequences of amino acids

Abstract

This paper introduces idiom networks of SCS (Short Constituent Sequences) for amino acid sequence analysis, where an idiom represents co-occurrence of two SCSs in a sequence. Thus, the idiom network proposed in this paper shows relations among idioms in an amino acid sequence. The authors also present an idiom network alignment problem, which may useful for protein sequence motif detection and its related purposes.

Search for Human-Specific Proteins Based on Availability Scores of Short Constituent Sequences: Identification of a WRWSH Protein in Human Testis

“…Assuming that small changes in amino acids in proteins (or corresponding nucleotide changes in DNA) contribute significantly to phenotypic differences between humans and chimpanzees, the concept of SCS-based methods is to detect small amino acid usage differences between species in an alignment-independent manner. The SCS package is an open web service containing six applications (plus the latest application to analyze idiom networks under development [55]) for protein analyses (http://scspackage.ads.ie.u-ryukyu.ac.jp/) [33]. These applications run in reference to the database downloaded from the nonredundant (nr) database of the NCBI (National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda), which was downloaded on August 20, 2015.…”