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Identification of regulatory elements is essential for understanding the mechanism behind regulating gene expression. These regulatory elements—located in or near gene—bind to proteins called transcription factors to initiate the transcription process. Their occurrences are influenced by the GC-content or nucleotide composition. For generating synthetic coding sequences with pre-specified amino acid sequence and desired GC-content, there exist two stochastic methods, multinomial and maximum entropy. Both methods rely on the probability of choosing the codon synonymous for usage in regard to a specific amino acid. In spite the latter exhibited unbiased manner, the produced sequences are not exactly obeying the GC-content constraint. In this paper, we present an algorithmic solution to produce coding sequences that follow exactly a primary amino acid sequence and a desired GC-content. The proposed tool, namely CodSeqGen, depends on random selection for smaller subsets to be traversed using the backtracking approach. • Generating random coding sequence is computationally expensive. • For proteins of length n , we need to test 6 n coding sequences to find those satisfying GC-content constraints. • CodSeqGen uses smart backtracking, and produces synonymous coding sequences with the exact desired GC-contents. • Experiments show CodSeqGen produces sequences with GC-contents that satisfy the constraints while NullSeq does not. [ABSTRACT FROM AUTHOR]

Abstract: The ARID is an ancient DNA-binding domain that is conserved throughout the evolution of higher eukaryotes. The ARID consensus sequence spans about 100 amino acid residues, and structural studies identify the major groove contact site as a modified helix-turn-helix motif. ARID-containing proteins exhibit a range of cellular functions, including participation in chromatin remodeling, and regulation of gene expression during cell growth, differentiation, and development. A subset of ARID family proteins binds DNA specifically at AT-rich sites; the remainder bind DNA nonspecifically. Orthologs to each of the seven distinct subfamilies of mammalian ARID-containing proteins are found in insect genomes, indicating the minimum age for the organization of these higher metazoan subfamilies. Many of these ancestral genes were duplicated and fixed over time to yield the 15 ARID-containing genes that are found in the human, mouse, and dog genomes. This paper describes a nomenclature, recommended by the Mouse Genomic Nomenclature Committee (MGNC) and accepted by the Human Genome Organization (HUGO) Gene Nomenclature Committee, for these mammalian ARID-containing genes that reflects this evolutionary history. [Copyright &y& Elsevier]