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Title 

New approach to the analysis of palindromic structure in genome sequences

 

genome sequence내의 palindrome 구조 분석을 위한 새로운 방법

Authors 

Seok-Won KimY S LeeSang-Haeng ChoiSung-Hwa ChaeDae-Won KimHong-Seog Park

Publisher 

Korea Genome Organization

Issue Date 

2006

Citation 

Genomics & Informatics, vol. 4, no. 4, pp. 167-169

Keywords 

palindromeinverted repeatBLAST

Abstract 

PABAP (Palindrome Analysis by BLAST Program) is an analysis system that identifies palindromic sequences from a large genome sequence up to several megabases long. It uses NCBI BLAST as a searching engine, and data processing such as alignment filtration and detection of inverted repeats which satisfy user- defined parameters is performed by manipulating data after populating into a MySQL database. PABAP outperforms publicly available palindrome search program in that it can detect large palindrome with internal spacer at a faster speed from bacterial genomes. It is a standalone application and is freely available for noncommercial users. Availability: This application was implemented with free software (Perl, Apache, MySQL, and NCBI BLAST) and is freely available to noncommercial users upon request. Analysis of user data can be carried out directly at http://chimp.kribb.re.kr/~javamint/palindrome.

ISSN 

1598-866X

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2019-05-02


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