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Bioinformatics. 2017 Jan 1;33(1):122-124. doi: 10.1093/bioinformatics/btw564. Epub 2016 Aug 26.

PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition.

Zuo Y1, Li Y1,2, Chen Y3, Li G1, Yan Z1,3, Yang L4.

Author information

1
The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, College of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
2
Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA.
3
School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
4
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.

Abstract

The reduced amino acids perform powerful ability for both simplifying protein complexity and identifying functional conserved regions. However, dealing with different protein problems may need different kinds of cluster methods. Encouraged by the success of pseudo-amino acid composition algorithm, we developed a freely available web server, called PseKRAAC (the pseudo K-tuple reduced amino acids composition). By implementing reduced amino acid alphabets, the protein complexity can be significantly simplified, which leads to decrease chance of overfitting, lower computational handicap and reduce information redundancy. PseKRAAC delivers more capability for protein research by incorporating three crucial parameters that describes protein composition. Users can easily generate many different modes of PseKRAAC tailored to their needs by selecting various reduced amino acids alphabets and other characteristic parameters. It is anticipated that the PseKRAAC web server will become a very useful tool in computational proteomics and protein sequence analysis.

AVAILABILITY AND IMPLEMENTATION:

Freely available on the web at http://bigdata.imu.edu.cn/psekraac CONTACTS: yczuo@imu.edu.cn or imu.hema@foxmail.com or yanglei_hmu@163.comSupplementary information: Supplementary data are available at Bioinformatics online.

PMID:
27565583
DOI:
10.1093/bioinformatics/btw564
[Indexed for MEDLINE]

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