rnammer RNAmmer predicts 5S/8S, 16S/18S, and 23S/2

功能简介

分析模块,默认输入Fasta格式的细菌完成图和草图组装结果。采用RNAmmer程序进行rRNA预测。封装了Software:rnammer-1.2。

RNAmmer  predicts ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov  Models:  An  initial  spotter  model searches  both  strands.  The  spotter model is constructed from highly conserved loci within a structural alignment of known  rRNA  sequences. Once  the  spotter  model  detects  an  approximate position of a gene, flanking regions are extracted and  parsed  to  the  full  model  which matches  the  entire  gene.   By  enabling  a  two-level approach it is avoided to run a full model through an entire genome sequence  allowing  faster predictions.


分析模块引用了 rnammer-1.2 软件(http://www.cbs.dtu.dk/services/RNAmmer/)。

相关文献如下所示:

Lagesen K, Hallin PF, Roedland E, Staerfeldt HH, Rognes T, Ussery DW. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 2007 Apr 22.