Development of TFSCAN as a program to search for DNA signals of TFSCAN = TFSCAN 검색 프로그램 TFSCAN의 개발

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Title
Development of TFSCAN as a program to search for DNA signals of TFSCAN = TFSCAN 검색 프로그램 TFSCAN의 개발
Author(s)
Byung Uk Lee; Kie Jung Park; Ki Bong Kim; W Park; Yong Ha Park
Bibliographic Citation
Korean Journal of (Applied) Microbiology & Biotechnology, vol. 24, no. 3, pp. 371-375
Publication Year
1996
Abstract
TFD is a transcription factor database which consists of short functional DNA sequences called as signals and their references. SIGNAL SCAN, developed by Dan S. Prestridge, is used to determine what signals of TFD may exist in a DNA sequence. This program searches TFD database by using a simple algorithm for character string comparison. We developed TFSCAN that aims at searching for signals in an input DNA sequence more efficently than SIGNAL SCAN. Our algorithms consist of two parts, one constructs an automata by scanning sequences of TFD, the other searches for signals through this automata. Searching for signal-related references is radically improved in time by using an indexing method. Usage of TFSCAN is very simple and its output is obvious. We developed and installed a TFSCAN input form and a CGI program in GINet Web server, to use TFSCAN. The algorithm applying automata showed drastical results in improvement of computing time. This approach may apply to recognizing several biological patterns. We have been developing our algorithm to optimize the automata and to search more sensitively for signals.
Keyword
AutomataCGI programSIGNAL SCANTFDTFSCANWWW
ISSN
0257-2389
Publisher
Korea Soc-Assoc-Inst
Type
Article
Appears in Collections:
1. Journal Articles > Journal Articles
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