Design and implementation of DB sequence optimization software.
- Author:
Long XU
1
;
Tao LI
;
Xiao-Wei ZHOU
;
Pei-Tang HUANG
Author Information
1. Beiing Institute of Biotechnology, Bejing 100071, China. xu_long@126.com
- Publication Type:Journal Article
- MeSH:
Base Sequence;
Codon;
genetics;
Programming Languages;
Protein Biosynthesis;
genetics;
Software
- From:
Chinese Journal of Biotechnology
2006;22(6):1032-1035
- CountryChina
- Language:Chinese
-
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.
