Commit 989974b7ccda91d5e48e1d5aeff85586f1117b1c - barrnap

Improve docs regarding Eukayrotic (Metazoan) rRNAs Torsten Seemann 7 years ago

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9	9
10	10	Barrnap predicts the location of ribosomal RNA genes in genomes.
11	11	It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S),
12		mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).
	12	metazoan mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).
13	13
14	14	It takes FASTA DNA sequence as input, and write GFF3 as output.
15	15	It uses the new NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style.

49	49	## Requirements
50	50
51	51	* Perl >= 5.6
52		* HMMER >= 3.1b
	52	* HMMER >= 3.1b (for `nhmmer`)
53	53
54	54	## License
55	55

57	57
58	58	## Comparison with RNAmmer
59	59
60		Barrnap is designed to be a substitute for RNAmmer. It was motivated by
61		my desire to remove <A HREF="https://github.com/tseemann/prokka">Prokka's</A> dependency on RNAmmer
62		which is encumbered by a free-for-academic sign-up license, and by RNAmmer's
63		dependence on legacy HMMER 2.x which conflicts with HMMER 3.x that most people are using now.
	60	Barrnap is designed to be a substitute for [RNAmmer](http://www.cbs.dtu.dk/services/RNAmmer/).
	61	It was motivated by my desire to remove [Prokka's](https://github.com/tseemann/prokka)
	62	dependency on RNAmmer which is encumbered by a free-for-academic sign-up
	63	license, and by RNAmmer's dependence on legacy HMMER 2.x which conflicts
	64	with HMMER 3.x that most people are using now.
64	65
65		RNAmmer is more sophisticated than Barrnap, and more accurate because it uses HMMER 2.x in glocal alignment mode whereas NHMMER 3.x currently only supports local alignment (Sean Eddy expects glocal to be supported in 2014). In practice, Barrnap will find all the typical rRNA genes in a few seconds (in bacteria), but may get the end points out by a few bases and will probably miss wierd rRNAs. The HMM models it uses are derived from Rfam, Silva and RefSeq.
	66	RNAmmer is more sophisticated than Barrnap, and more accurate because it
	67	uses HMMER 2.x in glocal alignment mode whereas NHMMER 3.x currently only
	68	supports local alignment (Sean Eddy expected glocal to be supported in 2014,
	69	but it still isn't available in 2017).
	70	In practice, Barrnap will find all the typical rRNA genes in a few seconds
	71	(in bacteria), but may get the end points out by a few bases and will
	72	probably miss wierd rRNAs. The HMM models it uses are derived from Rfam,
	73	Silva and RefSeq.
66	74
67	75	## Data sources for HMM models
68	76

92	100	Mito
93	101	12S RefSeq (MT-RNR1, s-rRNA, rns)
94	102	16S RefSeq (MT-RNR2, l-rRNA, rnl)
	103	</pre>
95	104
96		TODO: [Sajeet Haridas]
97		Fungi
	105	## Models I would like to add
	106
	107	<pre>
	108	Fungi [Sajeet Haridas]
98	109	LSU 35S ?
99	110	5S
100	111	5.8S

105	116	15S
106	117	21S (multiple exons)
107	118
108
109		TODO:
110	119	Apicoplast [http://www.ncbi.nlm.nih.gov/nuccore/U87145.2]
111	120	LSU ~2500bp 28S ?
112	121	SSU ~1500bp 16S ?
113	122
114		Plastid [Shaun Jackman]
115		?
116
	123	Plant [Shaun Jackman]
	124	Mito [https://www.ncbi.nlm.nih.gov/nucleotide?cmd=Retrieve&dopt=GenBank&list_uids=26556996]
	125	5S ~118 bp ? rrn5 (use RF00001 ?)
	126	18S ~1935 bp ? rrn18 (use RF01960 ?)
	127	26S ~2568 bp ? rrn26
117	128	</pre>
118	129
119	130	## Where does the name come from?