GenDBWiki/CoreDocumentation/RegionPrediction - Revision history

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2011-10-26T06:16:41Z

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← Older revision	Revision as of 08:16, 26 October 2011
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imported>LutzKrause at 12:44, 27 March 2006

2006-03-27T12:44:13Z

← Older revision		Revision as of 14:44, 27 March 2006
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	-n Do not run autoannotation <br>		-n Do not run autoannotation <br>
	-f restart failed, submitted or finished jobs <br>		-f restart failed, submitted or finished jobs <br>

			REGANOR is also available as a web-server at: https://www.cebitec.uni-bielefeld.de/groups/brf/software/reganor/index.html

	<span id="glimmer"></span>		<span id="glimmer"></span>

imported>AliceMcHardy at 10:32, 23 November 2004

2004-11-23T10:32:28Z

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imported>AliceMcHardy at 09:59, 23 November 2004

2004-11-23T09:59:42Z

← Older revision		Revision as of 11:59, 23 November 2004
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	\| (http://bioinformatics.oupjournals.org/cgi/reprint/20/10/1622)		\| (http://bioinformatics.oupjournals.org/cgi/reprint/20/10/1622)
	\|-		\|-
	\| Glimmer-2.1		\| [[#glimmer\|Glimmer-2.1]]
	\| Prediction of CDSs		\| Prediction of CDSs
	\| (http://nar.oupjournals.org/cgi/content/full/27/23/4636)		\| (http://nar.oupjournals.org/cgi/content/full/27/23/4636)
	\|-		\|-
	\| Critica		\| [[#critica\|Critica]]
	\| Prediction of CDSs, RBSs, Frameshifts		\| Prediction of CDSs, RBSs, Frameshifts
	\| (http://mbe.oupjournals.org/cgi/reprint/16/4/512)		\| (http://mbe.oupjournals.org/cgi/reprint/16/4/512)
	\|-		\|-
	\| RBSFinder		\| [[#rbsfinder\|RBSFinder]]
	\| Relocation of CDS starts, Prediction of RBSs		\| Relocation of CDS starts, Prediction of RBSs
	\| (http://bioinformatics.oupjournals.org/cgi/reprint/17/12/1123)		\| (http://bioinformatics.oupjournals.org/cgi/reprint/17/12/1123)
	\|-		\|-
	\| SearchforRNAs		\| [[#sfr\|SearchforRNAs]]
	\| Prediction of t- and rRNAs		\| Prediction of t- and rRNAs
	\| (Niels Larsen, University Aarhus, Denmark)		\| (Niels Larsen, University Aarhus, Denmark)
	\|-		\|-
	\| tRNAscan-SE		\| [[#trnascan\|tRNAscan-SE]]
	\| Prediction of tRNAs		\| Prediction of tRNAs
	\| (http://nar.oupjournals.org/cgi/content/full/25/5/955)		\| (http://nar.oupjournals.org/cgi/content/full/25/5/955)
	\|-		\|-
	\| Getorf		\| [[#getorf\|Getorf]]
	\| Lists all ORFs		\| Lists all ORFs
	\| (Contained in EMBOSS package, http://www.hgmp.mrc.ac.uk/Software/EMBOSS/)		\| (Contained in EMBOSS package, http://www.hgmp.mrc.ac.uk/Software/EMBOSS/)
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	in an extensive evaluation on 113 microbial genome sequences was shown to have a significantly improved		in an extensive evaluation on 113 microbial genome sequences was shown to have a significantly improved
	overall performance compared to the Glimmer standard application, especially for GC rich genomes.		overall performance compared to the Glimmer standard application, especially for GC rich genomes.
	For the prediction of tRNA genes, tRNAscan-SE is run. For the prediction of ~~tRNA~~ genes, tRNAscan-SE ~~is run~~.		For the prediction of tRNA genes, tRNAscan-SE is run. For the prediction of RNA genes, SearchForRNAs is run, which
	Based on the observations from the different CDS and ~~tRNA~~ genes are automatically annotated. Besides the		uses tRNAscan-SE. Based on the observations from the different CDS and RNA genes are automatically annotated.
	Critica predicted CDSs, additional Glimmer(ct) ~~predictions~~ which do not overlap more than 50bps with these		Besides the Critica predicted CDSs, additional Glimmer(ct) predicted CDSs which do not overlap more than 50bps with these
	are annotated. This way sensitivity compared to Critica is increased without significantly losing in specificity.		are annotated. This way, sensitivity compared to Critica is increased without significantly losing in specificity.
	The reliability of the different predictions is reflected by the 'status region' of these regions. CDSs		The reliability of the different predictions is reflected by the 'status region' of these regions. CDSs
	predicted by Critica are assigned 'status 2', additional annotated Glimmer(ct) predictions with high 'Vote		predicted by Critica are assigned 'status 2', additional annotated Glimmer(ct) predictions with high 'Vote
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	-r region - Contig to be analyzed - or - <br>		-r region - Contig to be analyzed - or - <br>
	-a run on all contigs <br>		-a run on all contigs <br>
	~~-t skip tRNAscan-SE <br>~~
	-n Do not run autoannotation <br>		-n Do not run autoannotation <br>
	-f restart failed jobs <br>		-f restart failed, submitted or finished jobs <br>

			<span id="glimmer"></span>
	=== GLIMMER-2.1 ===		=== GLIMMER-2.1 ===

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	(out of 99).		(out of 99).

			<span id="critica"></span>
	=== CRITICA ===		=== CRITICA ===

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	which is not really what the program is intended for.		which is not really what the program is intended for.

			<span id="rbsfinder"></span>
	=== RBSFinder ===		=== RBSFinder ===

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	2 1214 3010		2 1214 3010

			<span id="sfr"></span>
	=== SearchforRNAs ===		=== SearchforRNAs ===

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	predictions per tRNA identification)		predictions per tRNA identification)

			<span id="getorf"></span>
	=== Getorf ===		=== Getorf ===

imported>AlexanderGoesmann at 07:35, 17 November 2004

2004-11-17T07:35:09Z

← Older revision	Revision as of 09:35, 17 November 2004
(No difference)

Unknown user at 00:00, 1 January 1970

1970-01-01T00:00:00Z

New page

__NOTOC__
= Documentation for the GenDB Gene Finding Components =

== Currently integrated programs ==

{| border="1" cellpadding="2" cellspacing="0"
| '''Program'''
| '''Task'''
| '''Reference'''
|-
| [[#reganor|REGANOR]]
| Prediction of CDSs
| (http://bioinformatics.oupjournals.org/cgi/reprint/20/10/1622)
|-
| Glimmer-2.1
| Prediction of CDSs
| (http://nar.oupjournals.org/cgi/content/full/27/23/4636)
|-
| Critica
| Prediction of CDSs, RBSs, Frameshifts
| (http://mbe.oupjournals.org/cgi/reprint/16/4/512)
|-
| RBSFinder
| Relocation of CDS starts, Prediction of RBSs
| (http://bioinformatics.oupjournals.org/cgi/reprint/17/12/1123)
|-
| SearchforRNAs
| Prediction of t- and rRNAs
| (Niels Larsen, University Aarhus, Denmark)
|-
| tRNAscan-SE
| Prediction of tRNAs
| (http://nar.oupjournals.org/cgi/content/full/25/5/955)
|-
| Getorf
| Lists all ORFs
| (Contained in EMBOSS package, http://www.hgmp.mrc.ac.uk/Software/EMBOSS/)
|}

== Documentation for individual programs ==

In the following sections you can find detailed descriptions for all programs that can be used to predict regions within GenDB.



=== REGANOR ===

Reganor is a pipeline which automates the complete gene finding procedure for a sequence within GenDB.
For CDS prediction, a combined strategy based on the gene finders Glimmer and Critica applied. Glimmer is
run using the Critica predictions on the sequence as a training set of CDSs. This
in an extensive evaluation on 113 microbial genome sequences was shown to have a significantly improved
overall performance compared to the Glimmer standard application, especially for GC rich genomes.
For the prediction of tRNA genes, tRNAscan-SE is run. For the prediction of tRNA genes, tRNAscan-SE is run.
Based on the observations from the different CDS and tRNA genes are automatically annotated. Besides the
Critica predicted CDSs, additional Glimmer(ct) predictions which do not overlap more than 50bps with these
are annotated. This way sensitivity compared to Critica is increased without significantly losing in specificity.
The reliability of the different predictions is reflected by the 'status region' of these regions. CDSs
predicted by Critica are assigned 'status 2', additional annotated Glimmer(ct) predictions with high 'Vote
Scores' are assigned 'status 1', low scoring additional Glimmer(ct)-based annotations are assigned
'attention needed', as besides some true positive predictions the latter is likely to contain also some
false positive predictions.

Usage: reganor.pl -p <project name> (-r <region> | -a) [-t -f -n] 
where 
-p project name - the GenDB project to be run on
-r region - Contig to be analyzed - or - 
-a run on all contigs 
-t skip tRNAscan-SE 
-n Do not run autoannotation 
-f restart failed jobs 

=== GLIMMER-2.1 ===

The complete Glimmer package is integrated into GenDB in a comfortable manner. A Glimmer tool optimally
configured according to the evaluation given in [[McHardy]] et al. (Bioinformatics, 2004) can be
created with the default_tool_creation script or simply by using reganor.pl, where this tool
will be created and run along with the other gene finding programs of the default GenDB gene finding
pipeline. Configuration of individually designed Glimmer tools can be done via the [[ToolConfigurationWizard]]
in the graphical user interface. All options currently configurable are explicitly specified in this
interface. Note that there is an additional wrapper around the Glimmer functionality, which does not
recognize the options which can be given directly to the glimmer2 program, so do not specify such
options as 'other command line options'. What follows are extracts from the Glimmer
documentation and comments on how the programs are integrated within the GenDB system:

Glimmer 1.0 had 4 read me files, and Glimmer 2.0 maintains that
structure. The four main programs are:
# long-orfs
# extract
# build-icm
# glimmer2

1. Program long-orfs takes a sequence file (in FASTA format) and
outputs a list of all long "potential genes" in it that do not
overlap by too much. By "potential gene" I mean the portion of
an orf from the first start codon to the stop codon at the end.

2. Program extract takes a FASTA format sequence file and a file
with a list of start/stop positions in that file (e.g., as produced
by the long-orfs program) and extracts and outputs the
specified sequences.

3. Program build-icm.c creates and outputs an interpolated Markov
model (IMM) as described in the paper
A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg.
Improved Microbial Gene Identification with Glimmer.
Nucleic Acids Research, 1999, in press.

4. Program glimmer takes two inputs: a sequence file (in FASTA format)
and a collection of Markov models for genes as produced by the program
build-icm . It outputs a list of all open reading frames (orfs) together
with scores for each as a gene.

Comment: Programs 1-3 are used to create a model of CDS properties based on putative CDSs derived from
an input set of sequences. In GenDB, these are called the 'training sequences' and can be specified
during configuration (e.g. if multiple contigs belonging to one genome). By 'training tool', the method of how the putative CDSs
are extracted from these sequences is defined. If not choosing a 'training tool', the Glimmer default 'long-orfs' is applied.
The REGANOR wizard uses the gene finder Critica as the default 'training tool'. During the Glimmer tool run, glimmer2 is
then used with the ICM-model created in the training phase on the sequence specified to be analyzed.

Output:
The extended output resulting from a Glimmer run contains for every prediction three kind of scores: a probability,
a 'Vote Score' (stored as the 'result') and a 'Raw Score' (stored in GenDB along with other comments from the Glimmer
output as 'comment').

Configurable options:

Training tool: Any CDS prediction method for which observations on the specified
training sequence exist.
Training sequence: GenDB regions or an external sequence file in FASTA format.
For external sequences long orfs will be used as training
tool.

Look for RBS in start prediction Yes/ No along with pattern to search for.

Minimum gene length: Minimum length of genes to be predicted.

Linear region: vs. circular, with genes being predicted over the end of
the sequence.

Threshold: Probability score cut-off for prediction. Default is 90
(out of 99).

=== CRITICA ===

Critica is part of the GenDB default gene finding pipeline usable with the Reganor Wizard.
Different options from the default are configurable versus the [[ToolCreationWizard]].
Critica as integrated into GenDB does not allow separation of the training and prediction step. If
you want to run it for a set of smaller contigs from one genome, the best way to do this is by 'chaining'
the contigs together with linkers (containing stops in every frame) during the import into the GenDB system.

Output:
Observations resulting from a Critica run includes predicted CDSs, predicted ribosome binding sites and
predictions of possible frameshifts. The value stored under 'results' for the CDS predictions in GenDB
is the P-value given in the Critica output: The P-value is the amount of statistical support for the coding
region. Like BLAST, low scores are better.

Configurable options:

Look for RBS in start detection Use ribosome binding pattern to choose start

Note:
If Critica does not detect any CDSs, it dies with an error message, although this is not
really an error -- the result is that the corresponding GenDB job is assigned the state 'failed.
This is most likely to happen if you are trying to analyze very short sequences <= 10000bps with Critica,
which is not really what the program is intended for.

=== RBSFinder ===

From the documentation:
The program "rbs_finder.pl" implements an algorithm to find
ribosome binding sites (RBS) in the upstream regions of the
genes annotated by Glimmer2, [[GeneMark]], or other prokaryotic
gene finders. If there is no RBS-like patterns in this
region, program searches for a start codon having a RBS-like
pattern,in the same reading frame upstream or downstream
and relocates start codon accordingly.

Explanations for some directly configurable options in the [[ToolConfigurationWizard]]:

Window Size This parameter determines how
far the program should look for RBS-like pattern in
the upstream region of each of the genes. The best
results obtained using a window size of 50bps.

Iterations RBSsfinder achieves better results if run iteratively.

RBSFinder options configurable as 'other command-line options':

<Consensus_seq>: The default consensus
sequence is ("aggag"). However a computed sequence can
be used to get better results. The method to compute
the consensus sequence is as follows: -Take
the complement of last 30bps of 16S rRNA -
Find the most abundantly found 5bps subsequence of this
complement in the 30bps upstream regions of the start
codons annotated by Glimmer2. -Use this
sequence as consensus sequence.
<Partial_Coord_File>:The coordinates
that user wants to relocate or check for RBS site,
which can be a subset of coordinates annotated by
Glimmer2.This file should be in following format:

<Gene id> <Start Codon Coord> <Stop Codon Coord>
1 1030 1140
2 1214 3010

=== SearchforRNAs ===

From the documentation:
Searches a fasta formatted contig file for RNA's and prints tbl
style output. It works by using the RNA's from a set of closest
(or explicitly named) organisms as search probes and then tries
to guess the ends if the matches are not perfect. search_for_rnas
includes a run of tRNAscan-SE.

Configurable options:
Type of RNA D = all; a string like "tRNA, 16S, 23S, 5S"
Organism ID D = none; Give your organism an ID like "EC", "BS" ..
Domain D = all; phylogenetic domain of organism, A,B,E
Organism Genus D = all; genus name of organism
Organism Species D = all; species name of organism

Other command line options:
--probes D = none; an organism name, or part of
--complete D = 95; min. pct completeness of probe sequence(s)

=== tRNAscan-SE ===
From the documentation:

tRNAscan-SE combines the specificity of the Cove probabilistic RNA
prediction package (1) with the speed and sensitivity of tRNAscan 1.3
(2) plus an implementation of an algorithm described by Pavesi and
colleagues (3), which searches for eukaryotic pol III tRNA promoters
(our implementation referred to as EufindtRNA). tRNAscan and
EufindtRNA are used as first-pass prefilters to identify "candidate"
tRNA regions of the sequence. These subsequences are then passed to
Cove for further analysis, and output if Cove confirms the initial
tRNA prediction. In this way, tRNAscan-SE attains the best of both
worlds: (1) a false positive rate equally low to using Cove analysis,
(2) the combined sensitivities of tRNAscan and EufindtRNA (detection
of 98-99% of true tRNAs), and (3) search speed 1,000 to 3,000 times
faster than Cove analysis and 30 to 90 times faster than the original
tRNAscan 1.3 (tRNAscan-SE uses both a code-optimized version of
tRNAscan 1.3 which gives a 300-fold increase in speed, and a fast C
implementation of the Pavesi et al. algorithm).

Note: The current version of tRNAscan-Se (v 1.21) fails on sequences containing
non ATGC characters. Within the reganor pipeline, tRNAscan is
only included if the sequences do not contain such characters.

Configurable as additional options:

-B or -P : search for bacterial tRNAs (use bacterial tRNA model)
-A : search for archaeal tRNAs (use archaeal tRNA model)
-O : search for organellar (mitochondrial/chloroplast) tRNAs
-G : use general tRNA model (cytoplasmic tRNAs from all 3 domains included)

-C : search using covariance model analysis only (max sensitivity, slow)

-H : show both primary and secondary structure components to
covariance model bit scores
-D : disable pseudogene checking

Specify Alternate Cutoffs / Data Files:

-X <score> : set cutoff score (in bits) for reporting tRNAs (default=20)
-L <length>: set max length of tRNA intron+variable region (default=116bp)

-I <score> : manually set "intermediate" cutoff score for EufindtRNA
-z <number> : use <number> nucleotides padding when passing first-pass
tRNA bounds predictions to CM analysis (default=7)

-g <file> : use alternate genetic codes specified in <file> for
determining tRNA type
-c <file> : use an alternate covariance model in <file>

Misc Options:

-h : print this help message
-Q : do not prompt user before overwriting pre-existing
result files (for batch processing)

-n <EXPR> : search only sequences with names matching <EXPR> string
(<EXPR> may contain * or ? wildcard chars)
-s <EXPR> : start search at sequence with name matching <EXPR> string
and continue to end of input sequence file(s)
Special Options (for testing & special purposes)

-T : search using tRNAscan only (defaults to strict params)
-t <mode> : explicitly set tRNAscan params, where <mode>=R or S
(R=relaxed, S=strict tRNAscan v1.3 params)

-E : search using Eukaryotic tRNA finder (EufindtRNA) only
(defaults to Normal seach parameters when run alone,
or to Relaxed search params when run with Cove)
-e <mode> : explicitly set EufindtRNA params, where <mode>=R, N, or S
(relaxed, normal, or strict)

-r <file> : save first-pass scan results from EufindtRNA and/or
tRNAscan in <file> in tabular results format
-u <file> : search with Cove only those sequences & regions delimited
in <file> (tabular results file format)
-F <file> : save first-pass candidate tRNAs in <file> that were then
found to be false positives by Cove analysis
-M <file> : save all seqs that do NOT have at least one
tRNA prediction in them (aka "missed" seqs)
-v <file> : save verbose tRNAscan 1.3 output to <file>
-V <vers> : run an alternate version of tRNAscan
where <vers> = 1.3, 1.39, 1.4 (default), or 2.0
-K : Keep redundant tRNAscan 1.3 hits (don't filter out multiple
predictions per tRNA identification)

=== Getorf ===

Besides the options which can be chosen directly, additional options for this program which
can be specified as 'additional command line options' during tool configuration
with the [[ToolConfigurationWizard]]:

-maxsize integer Maximum nucleotide size of ORF to report
-find menu This is a small menu of possible output
options. The first four options are to
select either the protein translation or the
original nucleic acid sequence of the open
reading frame. There are two possible
definitions of an open reading frame: it can
either be a region that is free of STOP
codons or a region that begins with a START
codon and ends with a STOP codon. The last
three options are probably only of interest
to people who wish to investigate the
statistical properties of the regions around
potential START or STOP codons. The last
option assumes that ORF lengths are
calculated between two STOP codons.

-[no]methionine boolean START codons at the beginning of protein
products will usually code for Methionine,
despite what the codon will code for when it
is internal to a protein. This qualifier
sets all such START codons to code for
Methionine by default.
-[no]reverse boolean Set this to be false if you do not wish to
find ORFs in the reverse complement of the
sequence.
-flanking integer If you have chosen one of the options of the
type of sequence to find that gives the
flanking sequence around a STOP or START
codon, this allows you to set the number of
nucleotides either side of that codon to
output. If the region of flanking
nucleotides crosses the start or end of the
sequence, no output is given for this codon.