Method for the design of mRNA detecting genechip based on codon usage bias

Jianmin Ma; Wanjun Gu; Tong Zhou; Xiao Sun; Zuhong Lu

Method for the design of mRNA detecting genechip based on codon usage bias

Jianmin Ma, Wanjun Gu, Tong Zhou, Xiao Sun, Zuhong Lu

Research output: Contribution to journal › Article › peer-review

Abstract

To decrease the number of possibl probles during the process of chip design, the codon use frequency table of the to-be-detect mRNA sequence was first forecasted, and the coding codons for each amino acid were predicted. By this method, the number of probes was reduced to 4.47%. At the same time, such codon usage principles as C-G separation and G-T base-pairing were also considered. As a result, the number of probes was decreased to 4.25%. The optimum codon usage table was used to dramatically decrease the number of probes to 0.20% when the specificity of probes was not strictly demanded. As a result, the detecting information per square unit on genechip can be increased significantly.

Original language	English (US)
Pages (from-to)	581-585
Number of pages	5
Journal	Dongnan Daxue Xuebao (Ziran Kexue Ban)/Journal of Southeast University (Natural Science Edition)
Volume	32
Issue number	4
State	Published - Jul 2002
Externally published	Yes

Keywords

C-G selective separation
Codon usage bias
G-T base-pairing
Probe optimization
mRNA detecting genechip

ASJC Scopus subject areas

General Engineering

Cite this

@article{fd782beecd1847d9bd0b51fa847f75fb,

title = "Method for the design of mRNA detecting genechip based on codon usage bias",

abstract = "To decrease the number of possibl probles during the process of chip design, the codon use frequency table of the to-be-detect mRNA sequence was first forecasted, and the coding codons for each amino acid were predicted. By this method, the number of probes was reduced to 4.47%. At the same time, such codon usage principles as C-G separation and G-T base-pairing were also considered. As a result, the number of probes was decreased to 4.25%. The optimum codon usage table was used to dramatically decrease the number of probes to 0.20% when the specificity of probes was not strictly demanded. As a result, the detecting information per square unit on genechip can be increased significantly.",

keywords = "C-G selective separation, Codon usage bias, G-T base-pairing, Probe optimization, mRNA detecting genechip",

author = "Jianmin Ma and Wanjun Gu and Tong Zhou and Xiao Sun and Zuhong Lu",

year = "2002",

month = jul,

language = "English (US)",

volume = "32",

pages = "581--585",

journal = "Dongnan Daxue Xuebao (Ziran Kexue Ban)/Journal of Southeast University (Natural Science Edition)",

issn = "1001-0505",

publisher = "Southeast University",

number = "4",

}

TY - JOUR

T1 - Method for the design of mRNA detecting genechip based on codon usage bias

AU - Ma, Jianmin

AU - Gu, Wanjun

AU - Zhou, Tong

AU - Sun, Xiao

AU - Lu, Zuhong

PY - 2002/7

Y1 - 2002/7

N2 - To decrease the number of possibl probles during the process of chip design, the codon use frequency table of the to-be-detect mRNA sequence was first forecasted, and the coding codons for each amino acid were predicted. By this method, the number of probes was reduced to 4.47%. At the same time, such codon usage principles as C-G separation and G-T base-pairing were also considered. As a result, the number of probes was decreased to 4.25%. The optimum codon usage table was used to dramatically decrease the number of probes to 0.20% when the specificity of probes was not strictly demanded. As a result, the detecting information per square unit on genechip can be increased significantly.

AB - To decrease the number of possibl probles during the process of chip design, the codon use frequency table of the to-be-detect mRNA sequence was first forecasted, and the coding codons for each amino acid were predicted. By this method, the number of probes was reduced to 4.47%. At the same time, such codon usage principles as C-G separation and G-T base-pairing were also considered. As a result, the number of probes was decreased to 4.25%. The optimum codon usage table was used to dramatically decrease the number of probes to 0.20% when the specificity of probes was not strictly demanded. As a result, the detecting information per square unit on genechip can be increased significantly.

KW - C-G selective separation

KW - Codon usage bias

KW - G-T base-pairing

KW - Probe optimization

KW - mRNA detecting genechip

UR - http://www.scopus.com/inward/record.url?scp=0036660725&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0036660725&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:0036660725

SN - 1001-0505

VL - 32

SP - 581

EP - 585

JO - Dongnan Daxue Xuebao (Ziran Kexue Ban)/Journal of Southeast University (Natural Science Edition)

JF - Dongnan Daxue Xuebao (Ziran Kexue Ban)/Journal of Southeast University (Natural Science Edition)

IS - 4

ER -

Method for the design of mRNA detecting genechip based on codon usage bias

Abstract

Keywords

ASJC Scopus subject areas

Other files and links

Fingerprint

Cite this