GeMoMa - Revision history

Keilwagen: /* In a nutshell */

2022-07-16T20:02:57Z

In a nutshell

← Older revision		Revision as of 20:02, 16 July 2022
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	GeMoMa is a modular, homology-based gene prediction program with huge flexibility. However, we also provide a pipeline allowing to use GeMoMa easily. If you like to start GeMoMa for the first time, we recommend to use the GeMoMaPipeline like this		GeMoMa is a modular, homology-based gene prediction program with huge flexibility. However, we also provide a pipeline allowing to use GeMoMa easily. If you like to start GeMoMa for the first time, we recommend to use the GeMoMaPipeline like this
	java -jar GeMoMa-1.8.jar CLI GeMoMaPipeline threads=<threads> outdir=<outdir> GeMoMa.Score=ReAlign AnnotationFinalizer.r=NO o=true t=<target_genome> i=<reference_1_id> a=<reference_1_annotation> g=<reference_1_genome>		java -jar GeMoMa-1.9.jar CLI GeMoMaPipeline threads=<threads> outdir=<outdir> GeMoMa.Score=ReAlign AnnotationFinalizer.r=NO o=true t=<target_genome> i=<reference_1_id> a=<reference_1_annotation> g=<reference_1_genome>
	there are several parameters that need to be set indicated with '''<'''foo'''>'''. You can specify		there are several parameters that need to be set indicated with '''<'''foo'''>'''. You can specify
	* the number of threads		* the number of threads

Keilwagen: /* Version history */

2022-07-16T20:02:24Z

Version history

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 == Version history ==
-[http://www.jstacs.de/download.php?which=GeMoMa GeMoMa 1.8] (07.10.2021)
+[http://www.jstacs.de/download.php?which=GeMoMa GeMoMa 1.9] (15.07.2022)
 * extended manual
 * new module Analyzer: for benchmarking
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 * SyntenyChecker: implemented check of regular expression for prefix
-[http://www.jstacs.de/downloads/GeMoMa-1.7.zip GeMoMa 1.7.1] (07.09.2020)
+[http://www.jstacs.de/downloads/GeMoMa-1.7,1.zip GeMoMa 1.7.1] (07.09.2020)
 *GeMoMa:
 **bugfix if assignment == null

Keilwagen: /* GFF attributes */ 1.8

2021-10-07T12:23:45Z

GFF attributes: 1.8

← Older revision		Revision as of 12:23, 7 October 2021
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	== GFF attributes ==		== GFF attributes ==

	Using GeMoMa, you'll obtain GFFs containing some special attributes. We briefly explain the most prominent attributes in the following table.		Using GeMoMa and GAF, you'll obtain GFFs containing some special attributes. We briefly explain the most prominent attributes in the following table.

	{\| class="wikitable sortable"		{\| class="wikitable sortable"
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	!Attribute !!Long name !!Tool !!Necessary parameter !!Feature !!Description		!Attribute !!Long name !!Tool !!Necessary parameter !!Feature !!Description
	\|-		\|-
	\| aa \|\| amino acids \|\| GeMoMa \|\| \|\| mRNA \|\| the number of amino acids in the protein		\| aa \|\| amino acids \|\| GeMoMa \|\| \|\| mRNA \|\| the number of amino acids in the predicted protein
			\|-
			\| raa \|\| reference amino acids \|\| GeMoMa \|\| \|\| mRNA \|\| the number of amino acids in the reference protein
	\|-		\|-
	\| score \|\| GeMoMa score \|\| GeMoMa \|\| \|\| mRNA \|\| score computed by GeMoMa using the substitution matrix, gap costs and additional penalties		\| score \|\| GeMoMa score \|\| GeMoMa \|\| \|\| mRNA \|\| score computed by GeMoMa using the substitution matrix, gap costs and additional penalties
			\|-
			\| maxScore \|\| maximal GeMoMa score \|\| GeMoMa \|\| \|\| mRNA \|\| maximal score which will be obtained by a prediction that is identical to the reference transcript
			\|-
			\| bestScore \|\| best GeMoMa score \|\| GeMoMa \|\| \|\| mRNA \|\| score of the best GeMoMa prediction of this transcript and this target organism
			\|-
			\| maxGap \|\| maximal gap \|\| GeMoMa \|\| \|\| mRNA \|\| length of the longest gap in the alignment between predicted and reference protein
			\|-
			\| lpm \|\| longest positive match \|\| GeMoMa \|\| \|\| mRNA \|\| length of the longest positive scoring match in the alignment between predicted and reference protein, i.e., each pair of amino acids in the match has a positive score
	\|-		\|-
	\| nps \|\| number of premature stops \|\| GeMoMa \|\| \|\| mRNA \|\| the number of premature stop codons in the prediction		\| nps \|\| number of premature stops \|\| GeMoMa \|\| \|\| mRNA \|\| the number of premature stop codons in the prediction
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	\| minSplitReads \|\| minimal split reads \|\| GeMoMa \|\| introns \|\| mRNA \|\| minimal number of split reads for any of the predicted introns per predicted transcript		\| minSplitReads \|\| minimal split reads \|\| GeMoMa \|\| introns \|\| mRNA \|\| minimal number of split reads for any of the predicted introns per predicted transcript
	\|-		\|-
	\| iAA \|\| identical amino acid \|\| GeMoMa \|\| ~~query proteins~~ \|\| mRNA \|\| percentage of identical amino acids between reference transcript and prediction		\| iAA \|\| identical amino acid \|\| GeMoMa \|\| protein alignment \|\| mRNA \|\| percentage of identical amino acids between reference transcript and prediction
	\|-		\|-
	\| pAA \|\| positive amino acid \|\| GeMoMa \|\| ~~query proteins~~ \|\| mRNA \|\| percentage of aligned positions between reference transcript and prediction yielding a positive score in the substitution matrix		\| pAA \|\| positive amino acid \|\| GeMoMa \|\| protein alignment \|\| mRNA \|\| percentage of aligned positions between reference transcript and prediction yielding a positive score in the substitution matrix
	\|-		\|-
	\| evidence \|\| \|\| GAF \|\| \|\| mRNA \|\| number of reference organisms that have a transcript yielding this prediction		\| evidence \|\| \|\| GAF \|\| \|\| mRNA \|\| number of reference organisms that have a transcript yielding this prediction

Keilwagen: /* Version history */ 1.8

2021-10-07T12:19:22Z

Version history: 1.8

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 == Version history ==
-[http://www.jstacs.de/download.php?which=GeMoMa GeMoMa 1.7.1] (07.09.2020)
+[http://www.jstacs.de/download.php?which=GeMoMa GeMoMa 1.8] (07.10.2021)
 *GeMoMa:
 **bugfix if assignment == null

Keilwagen: /* In a nutshell */

2021-10-07T12:15:01Z

In a nutshell

← Older revision		Revision as of 12:15, 7 October 2021
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	GeMoMa is a modular, homology-based gene prediction program with huge flexibility. However, we also provide a pipeline allowing to use GeMoMa easily. If you like to start GeMoMa for the first time, we recommend to use the GeMoMaPipeline like this		GeMoMa is a modular, homology-based gene prediction program with huge flexibility. However, we also provide a pipeline allowing to use GeMoMa easily. If you like to start GeMoMa for the first time, we recommend to use the GeMoMaPipeline like this
	java -jar GeMoMa-1.~~7.1~~.jar CLI GeMoMaPipeline threads=<threads> outdir=<outdir> GeMoMa.Score=ReAlign AnnotationFinalizer.r=NO o=true t=<target_genome> i=<reference_1_id> a=<reference_1_annotation> g=<reference_1_genome>		java -jar GeMoMa-1.8.jar CLI GeMoMaPipeline threads=<threads> outdir=<outdir> GeMoMa.Score=ReAlign AnnotationFinalizer.r=NO o=true t=<target_genome> i=<reference_1_id> a=<reference_1_annotation> g=<reference_1_genome>
	there are several parameters that need to be set indicated with '''<'''foo'''>'''. You can specify		there are several parameters that need to be set indicated with '''<'''foo'''>'''. You can specify
	* the number of threads		* the number of threads

Keilwagen: /* In a nutshell */

2020-09-09T12:21:00Z

In a nutshell

← Older revision		Revision as of 12:21, 9 September 2020
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	GeMoMa is a modular, homology-based gene prediction program with huge flexibility. However, we also provide a pipeline allowing to use GeMoMa easily. If you like to start GeMoMa for the first time, we recommend to use the GeMoMaPipeline like this		GeMoMa is a modular, homology-based gene prediction program with huge flexibility. However, we also provide a pipeline allowing to use GeMoMa easily. If you like to start GeMoMa for the first time, we recommend to use the GeMoMaPipeline like this
	java -jar GeMoMa-1.7.jar CLI GeMoMaPipeline threads=<threads> outdir=<outdir> GeMoMa.Score=ReAlign AnnotationFinalizer.r=NO o=true t=<target_genome> i=<reference_1_id> a=<reference_1_annotation> g=<reference_1_genome>		java -jar GeMoMa-1.7.1.jar CLI GeMoMaPipeline threads=<threads> outdir=<outdir> GeMoMa.Score=ReAlign AnnotationFinalizer.r=NO o=true t=<target_genome> i=<reference_1_id> a=<reference_1_annotation> g=<reference_1_genome>
	there are several parameters that need to be set indicated with '''<'''foo'''>'''. You can specify		there are several parameters that need to be set indicated with '''<'''foo'''>'''. You can specify
	* the number of threads		* the number of threads
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	If you like to specify the maximum intron length please consider the parameters <code>GeMoMa.m</code> and <code>GeMoMa.sil</code>.		If you like to specify the maximum intron length please consider the parameters <code>GeMoMa.m</code> and <code>GeMoMa.sil</code>.
	If you have RNA-seq data either from own experiments or publicly available data sets (cf. [https://www.ncbi.nlm.nih.gov/sra NCBI SRA], [https://www.ebi.ac.uk/ena EMBL-EBI ENA]), we recommend to use them. You need to map the data against the target genome with your favorite read mapper. In addition, we recommend to check the parameters of the section '''DenoiseIntrons'''.		If you have RNA-seq data either from own experiments or publicly available data sets (cf. [https://www.ncbi.nlm.nih.gov/sra NCBI SRA], [https://www.ebi.ac.uk/ena EMBL-EBI ENA]), we recommend to use them. You need to map the data against the target genome with your favorite read mapper. In addition, we recommend to check the parameters of the section '''DenoiseIntrons'''.


	The complete documentation describing all GeMoMa modules and all parameters can be accessed at [[GeMoMa-Docs]].		The complete documentation describing all GeMoMa modules and all parameters can be accessed at [[GeMoMa-Docs]].

Keilwagen: /* Version history */

2020-09-09T11:49:20Z

Version history

← Older revision		Revision as of 11:49, 9 September 2020
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	== Version history ==		== Version history ==
	[http://www.jstacs.de/download.php?which=GeMoMa GeMoMa 1.7.] (29.07.2020)		[http://www.jstacs.de/download.php?which=GeMoMa GeMoMa 1.7.1] (07.09.2020)
	GeMoMa 1.7. (29.07.2020)		*GeMoMa:
			**bugfix if assignment == null
			**bugfix remove toUpperCase
			*GeMoMaPipeline
			**Galaxy integration bugfix for hidden parameter restart
			**hide BLAST_PATH and MMSEQS_PATH from Galaxy integration
			**improved protocol output if threads=1
			**add addtional test to GeMoMaPipeline

			[http://www.jstacs.de/downloads/GeMoMa-1.7.zip GeMoMa 1.7] (29.07.2020)
	*improved manual including new module and runtime		*improved manual including new module and runtime
	*check whether input files exist before execution		*check whether input files exist before execution

Keilwagen: /* In a nutshell */

2020-09-03T05:46:22Z

In a nutshell

← Older revision		Revision as of 05:46, 3 September 2020
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	If you have RNA-seq data either from own experiments or publicly available data sets (cf. [https://www.ncbi.nlm.nih.gov/sra NCBI SRA], [https://www.ebi.ac.uk/ena EMBL-EBI ENA]), we recommend to use them. You need to map the data against the target genome with your favorite read mapper. In addition, we recommend to check the parameters of the section '''DenoiseIntrons'''.		If you have RNA-seq data either from own experiments or publicly available data sets (cf. [https://www.ncbi.nlm.nih.gov/sra NCBI SRA], [https://www.ebi.ac.uk/ena EMBL-EBI ENA]), we recommend to use them. You need to map the data against the target genome with your favorite read mapper. In addition, we recommend to check the parameters of the section '''DenoiseIntrons'''.

	The complete documentation describing all GeMoMa modules and all ~~paaremeters~~ can be accessed at [[GeMoMa-Docs]].		The complete documentation describing all GeMoMa modules and all parameters can be accessed at [[GeMoMa-Docs]].

	You can also [[:File:GeMoMa-manual.pdf\|download a small manual for GeMoMa]] which explains the main steps for the analysis.		You can also [[:File:GeMoMa-manual.pdf\|download a small manual for GeMoMa]] which explains the main steps for the analysis.

Keilwagen: /* Frequently asked questions */

2020-08-27T06:47:27Z

Frequently asked questions

← Older revision		Revision as of 06:47, 27 August 2020
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	:A restart of GeMoMaPipeline is particularly useful if the time-consuming search (tblastn or mmseqs) was successful, since this can save runtime.		:A restart of GeMoMaPipeline is particularly useful if the time-consuming search (tblastn or mmseqs) was successful, since this can save runtime.

	~~For~~ any further questions or ~~comments~~ please check [https://github.com/Jstacs/Jstacs/labels/GeMoMa our github page].		If you have any further questions, comments or bugs, please check the [[GeMoMa-Docs]], [https://github.com/Jstacs/Jstacs/labels/GeMoMa our github page] or contact [mailto:jens.keilwagen@julius-kuehn.de Jens Keilwagen].

	== References ==		== References ==

Keilwagen: /* Frequently asked questions */

2020-08-24T13:49:07Z

Frequently asked questions

← Older revision		Revision as of 13:49, 24 August 2020
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	:A restart of GeMoMaPipeline is particularly useful if the time-consuming search (tblastn or mmseqs) was successful, since this can save runtime.		:A restart of GeMoMaPipeline is particularly useful if the time-consuming search (tblastn or mmseqs) was successful, since this can save runtime.

	For any further questions or comments please ~~contact jens~~.~~keilwagen@julius-kuehn~~.de		For any further questions or comments please check [https://github.com/Jstacs/Jstacs/labels/GeMoMa our github page].

	== References ==		== References ==