title: [Design and implementation of DB sequence optimization software].
abstract: TIR (Translation Initiation Region) efficiency is very important in prokaryotic expression. The TIR's efficiency is highly dependent on SD (Shine-Dalgarno) sequence, distance between SD sequence and start codon, DB (Downstream Box) sequence, TIR's second structure, codon adaptation and so on. In this paper, we designed and implemented the software to optimize DB sequence and 5' rare codons. It generated some optimization sequences by analyzing the target sequence and comparing it with 16S RNA. And the optimization sequences is sorting by number of base pairing, location of base pairing and codon adaptation. We drew up the algorithm and the core of code in this paper.
authors.affiliation: Beiing Institute of Biotechnology, Bejing 100071, China. xu_long@126.com
authors.forename: Long
authors.initials: L
authors.lastname: Xu
authors.forename: Tao
authors.initials: T
authors.lastname: Li
authors.forename: Xiao-Wei
authors.initials: XW
authors.lastname: Zhou
authors.forename: Pei-Tang
authors.initials: PT
authors.lastname: Huang
mesh_terms: D001483:Base Sequence; D003062:Codon / Q000235:genetics; D011381:Programming Languages; D014176:Protein Biosynthesis / Q000235:genetics*; D012984:Software
chemical_list: D003062:Codon