taveRNA: a web suite for RNA algorithms and applications

被引：10

作者：

Aksay, Cagri ^{[1
]}

Salari, Raheleh ^{[1
]}

Karakoc, Emre ^{[1
]}

Alkan, Can ^{[1
]}

Sahinalp, S. Cenk ^{[1
]}

机构：

[1] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

来源：

NUCLEIC ACIDS RESEARCH | 2007年 / 35卷

基金：

加拿大创新基金会; 加拿大自然科学与工程研究理事会;

关键词：

D O I：

10.1093/nar/gkm303

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

xWe present taveRNA, a web server package that hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is a new alternative for RNA secondary structure prediction. It is based on a dynamic programming solution that minimizes the sum of energy density and free energy of an RNA structure. inteRNA is the first RNA-RNA interaction structure prediction web service. It also employs a dynamic programming algorithm to minimize the free energy of the resulting joint structure of the two interacting RNAs. Lastly, pRuNA is an efficient database pruning service; which given a query RNA, eliminates a significant portion of an ncRNA database and returns only a few ncRNAs as potential regulators. taveRNA is available at http://compbio.cs.sfu.ca/taverna.

引用

页码：W325 / W329

页数：5

共 15 条

[1]

AKSAY C, 2007, TR200706 SIM FRAS U

[2]

Alkan C, 2005, LECT NOTES COMPUT SC, V3500, P152

[3]

Alkan C, 2006, LECT NOTES COMPUT SC, V3909, P130, DOI 10.1007/11732990_12

[4]

Bafna V, 2005, LECT NOTES COMPUT SC, V3500, P172

[5]

BRUCCOLERI RE, 1988, COMPUT APPL BIOSCI, V4, P167

[6] Fewer genes, more noncoding RNA [J].

Claverie, JM .

SCIENCE, 2005, 309 (5740) :1529-1530

[7] Rfam: annotating non-coding RNAs in complete genomes [J].

Griffiths-Jones, S ;

Moxon, S ;

Marshall, M ;

Khanna, A ;

Eddy, SR ;

Bateman, A .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D121-D124

[8] THE EFFECT OF LOOP SIZE IN ANTISENSE AND TARGET RNAS ON THE EFFICIENCY OF ANTISENSE RNA CONTROL [J].

HJALT, T ;

WAGNER, EGH .

NUCLEIC ACIDS RESEARCH, 1992, 20 (24) :6723-6732

[9] Secondary structure prediction for aligned RNA sequences [J].

Hofacker, IL ;

Fekete, M ;

Stadler, PF .

JOURNAL OF MOLECULAR BIOLOGY, 2002, 319 (05) :1059-1066

[10]

LIN GH, 2001, P 5 ANN INT C COMP B, P211

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