【求助】根据基因组是否可以推算出其miRNA
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各位分子生物学大佬，本人目前才开始涉足miRNA，有诸多不懂之处，向各位请教。
1，目前研究微生物miRNA多集中在病毒上，为什么真菌，细菌，支原体等研究较少，难道仅仅是因为基因组大小不同吗？
2，查了下miRNA库，http://microrna.sanger.ac.uk/sequences/，似乎没有发现有关于真菌和某些细菌miRNA。请问：有没有这方面的生物信息学软件，根据微生物的基因组，预测其可能产生的miRNA（根据miRNA前体容易形成发夹状结构这一特点）。
1，目前研究微生物miRNA多集中在病毒上，为什么真菌，细菌，支原体等研究较少，难道仅仅是因为基因组大小不同吗？
2，查了下miRNA库，http://microrna.sanger.ac.uk/sequences/，似乎没有发现有关于真菌和某些细菌miRNA。请问：有没有这方面的生物信息学软件，根据微生物的基因组，预测其可能产生的miRNA（根据miRNA前体容易形成发夹状结构这一特点）。
是不是研究病毒更有意义？
qipeng1225 wrote:
是不是研究病毒更有意义？
终于有人回帖了，我还以为我的帖子太没有水平，大家都不屑于回答。
应该不是病毒更有意义，我觉得可能病毒基因组比较小，所以病毒miRNA可能数量较少，易于研究。另外，病毒是胞内寄生，可能鞥容易通过miRNA实现和宿主细胞的interaction。
回答正确，建议给斑竹和小弟各加一分。遥想当年，对病毒miRNA是如此的痴迷，写了中英文综述各一篇，现在，没有那么多精力去搞，也只能放弃。而且感觉现在这方面的研究越来越难，似乎能发现的DNA病毒编码的miRNA都被发现了，什么时候RNA病毒大声喊出来我有miRNA并且是我吃饭的家伙，那science才可能过来看看
hzdlj wrote:
终于有人回帖了，我还以为我的帖子太没有水平，大家都不屑于回答。
应该不是病毒更有意义，我觉得可能病毒基因组比较小，所以病毒miRNA可能数量较少，易于研究。另外，病毒是胞内寄生，可能鞥容易通过miRNA实现和宿主细胞的interaction。
Have you heard someone to study miRNAs in Bacteriophage? Which should not be bigger than virus.
The reason is that siRNA and miRNA need some protein complex such as Dicer and Ago encoded by eukaryote to function. These genes have not be identified in bacterial, so it's currently believed there are no siRNA and miRNA in bacterial and Bacteriophage.
http://www.mirz.unibas.ch/cgi/pred_miRNA_genes.cgi
有专门的miRNA预测服务：miRNA prediction with miR-abela
有专门的miRNA预测服务：miRNA prediction with miR-abela
alixtardxy wrote:
Have you heard someone to study miRNAs in Bacteriophage? Which should not be bigger than virus.
The reason is that siRNA and miRNA need some protein complex such as Dicer and Ago encoded by eukaryote to function. These genes have not be identified in bacterial, so it's currently believed there are no siRNA and miRNA in bacterial and Bacteriophage.
细菌里面有类似miRNA和siRNA的noncoding RNA，和细菌里面其他一些ncRNA一起被称为sRNA.
对miRNA来说，有很多预测其gene的软件，对sRNA的可以看看：
Small RNA gene identification and mRNA target predictions in bacteria
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/24/2807
还有一些预测sRNA target的工具：
Target prediction for small, noncoding RNAs in bacteria
http://nar.oxfordjournals.org/cgi/content/abstract/34/9/2791
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
http://bioinformatics.oxfordjournals.org/cgi/content/full/24/24/2849
sulicon wrote:
细菌里面有类似miRNA和siRNA的noncoding RNA，和细菌里面其他一些ncRNA一起被称为sRNA.
Small RNAs in bacteria are totally different from siRNAs and miRNAs. In most cases, these small moleculars will interfere the binding of ribosomes to mRNA to inhibit translation.
alixtardxy wrote:
Small RNAs in bacteria are totally different from siRNAs and miRNAs. In most cases, these small moleculars will interfere the binding of ribosomes to mRNA to inhibit translation.
支持alixtardxy 版主的看法。
小RNA研究主要是在真核生物中进行的。目前，还很少（据我所知，还没有）在原核生物中发现siRNA。microRNAs的情况大致相同。
alixtardxy wrote:
Small RNAs in bacteria are totally different from siRNAs and miRNAs. In most cases, these small moleculars will interfere the binding of ribosomes to mRNA to inhibit translation.
我没有说清楚。 我说类似 miRNA只是指它们也是行使转录后抑制的功能，就像你说的那样。摘抄一点introduction:
"In recent years, hundreds of RNAs that do not encode proteins but have intrinsic functions as regulators have been identified. These RNAs are generally denoted noncoding RNAs in eukaryotes and small RNAs (sRNAs) in bacteria. In Escherichia coli alone, >70 sRNA genes have been identified. Those bacterial sRNAs whose functions have been characterized can be sorted into three general categories: sRNAs that have intrinsic catalytic activity or are components of ribonucleoproteins, sRNAs that affect protein activity by structurally mimicking other nucleic acids and sRNAs that post-transcriptionally regulate mRNAs via basepairing interactions"
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