SFAPS: An R package for structure/function analysis of protein sequences based on informational spectrum method

被引：64

作者：

Deng, Su-Ping ^{[1
]}

Huang, De-Shuang ^{[1
,2
]}

机构：

[1] Tongji Univ, Coll Elect & Informat Engn, Machine Learning & Syst Biol Lab, Shanghai 201804, Peoples R China

[2] Zhengzhou Univ Light Ind, Coll Comp & Commun Engn, Zhengzhou 450002, Peoples R China

来源：

METHODS | 2014年 / 69卷 / 03期

基金：

美国国家科学基金会;

关键词：

R package; Structure/function analysis; Protein sequence; Informational spectrum method; HOT-SPOTS; IDENTIFICATION; PREDICTION; ENHANCER; BINDING;

D O I：

10.1016/j.ymeth.2014.08.004

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The R package SFAPS has been developed for structure/function analysis of protein sequences based on information spectrum method. The informational spectrum method employs the electron-ion interaction potential parameter as the numerical representation for the protein sequence, and obtains the characteristic frequency of a particular protein interaction after computing the Discrete Fourier Transform for protein sequences. The informational spectrum method is often used to analyze protein sequences, so we developed this software tool, which is implemented as an add-on package to the freely available and widely used statistical language R. Our package is distributed as open source code for Linux, Unix and Microsoft Windows. It is released under the GNU General Public License. (C) 2014 Elsevier Inc. All rights reserved.

引用

页码：207 / 212

页数：6

共 27 条

[1]

[Anonymous], 2002, Oxidative Phosphorylation

[2] The influenza virus resource at the national center for biotechnology information [J].

Bao, Yiming ;

Bolotov, Pavel ;

Dernovoy, Dmitry ;

Kiryutin, Boris ;

Zaslavsky, Leonid ;

Tatusova, Tatiana ;

Ostell, Jim ;

Lipman, David .

JOURNAL OF VIROLOGY, 2008, 82 (02) :596-601

[3] FLAN: a web server for influenza virus genome annotation [J].

Bao, Yiming ;

Bolotov, Pavel ;

Dernovoy, Dmitry ;

Kiryutin, Boris ;

Tatusova, Tatiana .

NUCLEIC ACIDS RESEARCH, 2007, 35 :W280-W284

[4]

Charles V.L., 2011, COMPUTATIONAL FRAMEW

[5] ENHANCER BINDING-PROTEINS PREDICTED BY INFORMATIONAL SPECTRUM METHOD [J].

COSIC, I ;

NESIC, D ;

PAVLOVIC, M ;

WILLIAMS, R .

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 1986, 141 (02) :831-838

[6] THE RELATIONSHIP OF THE RESONANT RECOGNITION MODEL TO EFFECTS OF LOW-INTENSITY LIGHT ON CELL-GROWTH [J].

COSIC, I ;

VOJISAVLJEVIC, V ;

PAVLOVIC, M .

INTERNATIONAL JOURNAL OF RADIATION BIOLOGY, 1989, 56 (02) :179-191

[7] PREDICTION OF HOT SPOTS IN SV40 ENHANCER AND RELATION WITH EXPERIMENTAL-DATA [J].

COSIC, I ;

NESIC, D .

EUROPEAN JOURNAL OF BIOCHEMISTRY, 1987, 170 (1-2) :247-252

[8] MACROMOLECULAR BIOACTIVITY - IS IT RESONANT INTERACTION BETWEEN MACROMOLECULES - THEORY AND APPLICATIONS [J].

COSIC, I .

IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, 1994, 41 (12) :1101-1114

[9] PREDICTION OF HOT SPOTS IN INTERLEUKIN-2 BASED ON INFORMATIONAL SPECTRUM CHARACTERISTICS OF GROWTH-REGULATING FACTORS - COMPARISON WITH EXPERIMENTAL-DATA [J].

COSIC, I ;

PAVLOVIC, M ;

VOJISAVLJEVIC, V .

BIOCHIMIE, 1989, 71 (03) :333-342

[10]

Cosic I., 1997, RESONANT RECOGNITION

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