Conserved RNA secondary structures in viral genomes: a survey

被引:37
作者
Hofacker, IL
Stadler, PF
Stocsits, RR
机构
[1] Univ Vienna, Inst Theoret Chem & Mol Strukturbiol, A-1090 Vienna, Austria
[2] Univ Leipzig, Inst Informat, D-04103 Leipzig, Germany
关键词
D O I
10.1093/bioinformatics/bth108
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The genomes of RNA viruses often carry conserved RNA structures that perform vital functions during the life cycle of the virus. Such structures can be detected using a combination of structure prediction and co-variation analysis. Here we present results from pilot studies on a variety of viral families performed during bioinformatics computer lab courses in past years.
引用
收藏
页码:1495 / 1499
页数:5
相关论文
共 16 条
[1]   SEQUENCE-ANALYSIS OF RNA SPECIES SYNTHESIZED BY Q-BETA REPLICASE WITHOUT TEMPLATE [J].
BIEBRICHER, CK ;
LUCE, R .
BIOCHEMISTRY, 1993, 32 (18) :4848-4854
[2]   The universal virus database ICTVdB [J].
Büchen-Osmond, C .
COMPUTING IN SCIENCE & ENGINEERING, 2003, 5 (03) :16-25
[3]  
CHEONG HK, 2003, NUCLEIC ACIDS RES, V27, P1392
[4]  
FAULSTICH LC, 2003, DATA MINING TEXT MIN, P20
[5]  
FEKETE M, 2000, THESIS U VIENNA
[6]   Automatic detection of conserved base pairing patterns in RNA virus genomes [J].
Hofacker, IL ;
Stadler, PF .
COMPUTERS & CHEMISTRY, 1999, 23 (3-4) :401-414
[7]   Automatic detection of conserved RNA structure elements in complete RNA virus genomes [J].
Hofacker, IL ;
Fekete, M ;
Flamm, C ;
Huynen, MA ;
Rauscher, S ;
Stolorz, PE ;
Stadler, PF .
NUCLEIC ACIDS RESEARCH, 1998, 26 (16) :3825-3836
[8]   The hepatitis B virus pregenome: Prediction of RNA structure and implications for the emergence of deletions [J].
Kidd-Ljunggren, K ;
Zuker, M ;
Hofacker, IL ;
Kidd, AH .
INTERVIROLOGY, 2000, 43 (03) :154-164
[9]   Hairpin loop structure in the 3′ arm of the influenza A virus virion RNA promoter is required for endonuclease activity [J].
Leahy, MB ;
Dobbyn, HC ;
Brownlee, GG .
JOURNAL OF VIROLOGY, 2001, 75 (15) :7042-7049
[10]   Noncoding RNA gene detection using comparative sequence analysis [J].
Rivas, Elena ;
Eddy, Sean R. .
BMC BIOINFORMATICS, 2001, 2 (1)