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This article mainly explains "how to use RNAmmer". The content in the article is simple and clear, and it is easy to learn and understand. Please follow the editor's train of thought to study and learn how to use RNAmmer.

RNAmmer is a special rRNA prediction tool. The training data set of hidden Markov model used in this software is 5S rRNA database and European rRNA database, which has high accuracy. It can be used to predict not only 5S, 16s and 23s rRNA of prokaryotes, but also 5S, 5.8s, 18s and 28s Rrna of eukaryotes, and it is not based on the ab initio prediction of reference sequences.

In order to download local use, you need to first fill in the name, mailbox, organization and other information on the website to apply, and then the software download link will be sent to the mailbox. You need to install Hmmer first, and then download and decompress the RNAmmer package and then use it. The method of use is as follows: rnammer-S bac-m lsu,ssu,tsu-xml out.xml-gff out.gff-h out.hmmreport-f out.rRNA.fasta genome.fasta-S specifies the bounds to which the species of the input sequence belongs: the type of rRNA that needs to be predicted by Archaea arc, bacterial bac or eukaryotic euk;-m: 'tsu' is 5pm 8s rRNA,'ssu', 16pm 18s rRNA,'lsu' and 23ram 28s rRNA. If all predictions are made, it will be set to 'tsu,ssu,lsu';-multi parallel operation, predict all rRNA on both positive and negative chains, and run up to 6 calculations in parallel, which is equivalent to-m lsu,ssu,tsu -fasta result file name of rRNA generated by f-hmm result report file name generated by h-gff2 file name of rRNA generated by gff-xml result file name generated by xml predicts the bacterial genome sequence as follows: rnammer-S bac-m lsu,ssu,tsu-gff twk.rRNA.gff-f twk.rRNA.fasta-h twk.rRNA.hmmreport new.scaffolds.fasta

The prediction results and sequences of 5S, 16s, 28s rRNA can be seen in the gff and fasta files, as follows:

In general, 23s rRNA and 5s rRNA are closely linked to each other in bacterial genome, while there is a long sequence segment between 23s rRNA and 16s human RNA. Thank you for your reading, the above is the content of "how to use RNAmmer", after the study of this article, I believe you have a deeper understanding of how to use RNAmmer, and the specific use needs to be verified in practice. Here is, the editor will push for you more related knowledge points of the article, welcome to follow!

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