GenDBWiki/CoreDocumentation/FunctionPrediction - Revision history

Admin: 21 revisions

2011-10-26T06:13:19Z

21 revisions

← Older revision	Revision as of 08:13, 26 October 2011
(No difference)

imported>LutzKrause at 12:45, 24 November 2004

2004-11-24T12:45:42Z

← Older revision	Revision as of 14:45, 24 November 2004
(No difference)

imported>LutzKrause at 17:02, 23 November 2004

2004-11-23T17:02:56Z

← Older revision		Revision as of 19:02, 23 November 2004
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	\| Search for transmembrane regions of proteins		\| Search for transmembrane regions of proteins
	\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11152613&itool=iconabstr TMHMM]		\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11152613&itool=iconabstr TMHMM]
	\|}		\|-
	-~~---- /!\ Edit conflict! Other version: -----~~
	~~{\| border="1" cellpadding="2" cellspacing="0"~~
	~~\| [[#hth\|Helixturnhelix]]~~
	~~\| Detection of helix-turn-helix nucleic acid binding motifs in proteins~~
	\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-40CRS27-G&_coverDate=06%2F01%2F2000&_alid=223069367&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5183&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=fcef5227189fa9f0d87d36eeb435c121 EMBOSS]
	\|}
	~~----- /!\ Edit conflict! Your version: -----~~
	~~{\| border="1" cellpadding="2" cellspacing="0"~~
	\| [[#hth\|Helixturnhelix]]		\| [[#hth\|Helixturnhelix]]
	\| Detection of helix-turn-helix nucleic acid binding motifs in proteins		\| Detection of helix-turn-helix nucleic acid binding motifs in proteins
	\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-40CRS27-G&_coverDate=06%2F01%2F2000&_alid=223069367&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5183&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=fcef5227189fa9f0d87d36eeb435c121 EMBOSS]		\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-40CRS27-G&_coverDate=06%2F01%2F2000&_alid=223069367&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5183&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=fcef5227189fa9f0d87d36eeb435c121 EMBOSS]
	\|}		\|}
	~~----- /!\ End of edit conflict -----~~

	== Documentation for individual programs ==		== Documentation for individual programs ==
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	SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences. Information about it can be found [http://www.cbs.dtu.dk/services/SignalP/ here]. The tool is not freely available therefore you have to send a request to the author in order to receive it.		SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences. Information about it can be found [http://www.cbs.dtu.dk/services/SignalP/ here]. The tool is not freely available therefore you have to send a request to the author in order to receive it.

	~~----- /!\ Edit conflict! Other version: -----~~
	<span id="hth"></span>		<span id="hth"></span>

	== Helixturnhelix ==		== Helixturnhelix ==

	Helixturnhelix is part of the EMBOSS package and finds helix-turn-helix nucleic acid binding motifs in proteins.		Helixturnhelix is part of the EMBOSS package and finds helix-turn-helix nucleic acid binding motifs in proteins. To use
			the program in GenDB you need to install the EMBOSS package from the MRC [http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/download.html download site].
	To use ~~Helixturnhelix in GenDB you need to install the EMBOSS package from the MRC [http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/download.html download site].~~
	~~----- /!\ Edit conflict! Your version: -----~~
	~~<span id="hth"></span>~~

	~~== Helixturnhelix ==~~

	~~Helixturnhelix is part of~~ the ~~EMBOSS package and finds helix-turn-helix nucleic acid binding motifs in proteins.~~

	~~To use Helixturnhelix~~ in GenDB you need to install the EMBOSS package from the MRC [http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/download.html download site].
	~~----- /!\ End of edit conflict -----~~

imported>LutzKrause at 16:58, 23 November 2004

2004-11-23T16:58:29Z

← Older revision		Revision as of 18:58, 23 November 2004
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	\| Search for transmembrane regions of proteins		\| Search for transmembrane regions of proteins
	\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11152613&itool=iconabstr TMHMM]		\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11152613&itool=iconabstr TMHMM]
	\|-		\|}
			----- /!\ Edit conflict! Other version: -----
			{\| border="1" cellpadding="2" cellspacing="0"
			\| [[#hth\|Helixturnhelix]]
			\| Detection of helix-turn-helix nucleic acid binding motifs in proteins
			\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-40CRS27-G&_coverDate=06%2F01%2F2000&_alid=223069367&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5183&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=fcef5227189fa9f0d87d36eeb435c121 EMBOSS]
			\|}
			----- /!\ Edit conflict! Your version: -----
			{\| border="1" cellpadding="2" cellspacing="0"
	\| [[#hth\|Helixturnhelix]]		\| [[#hth\|Helixturnhelix]]
	\| Detection of helix-turn-helix nucleic acid binding motifs in proteins		\| Detection of helix-turn-helix nucleic acid binding motifs in proteins
	\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-40CRS27-G&_coverDate=06%2F01%2F2000&_alid=223069367&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5183&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=fcef5227189fa9f0d87d36eeb435c121 EMBOSS]		\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-40CRS27-G&_coverDate=06%2F01%2F2000&_alid=223069367&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5183&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=fcef5227189fa9f0d87d36eeb435c121 EMBOSS]
	\|}		\|}
			----- /!\ End of edit conflict -----

	== Documentation for individual programs ==		== Documentation for individual programs ==
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	SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences. Information about it can be found [http://www.cbs.dtu.dk/services/SignalP/ here]. The tool is not freely available therefore you have to send a request to the author in order to receive it.		SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences. Information about it can be found [http://www.cbs.dtu.dk/services/SignalP/ here]. The tool is not freely available therefore you have to send a request to the author in order to receive it.

			----- /!\ Edit conflict! Other version: -----
			<span id="hth"></span>

			== Helixturnhelix ==

			Helixturnhelix is part of the EMBOSS package and finds helix-turn-helix nucleic acid binding motifs in proteins.

			To use Helixturnhelix in GenDB you need to install the EMBOSS package from the MRC [http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/download.html download site].
			----- /!\ Edit conflict! Your version: -----
	<span id="hth"></span>		<span id="hth"></span>

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	To use Helixturnhelix in GenDB you need to install the EMBOSS package from the MRC [http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/download.html download site].		To use Helixturnhelix in GenDB you need to install the EMBOSS package from the MRC [http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/download.html download site].
			----- /!\ End of edit conflict -----

imported>LutzKrause at 16:57, 23 November 2004

2004-11-23T16:57:57Z

← Older revision		Revision as of 18:57, 23 November 2004
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	\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11152613&itool=iconabstr TMHMM]		\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11152613&itool=iconabstr TMHMM]
	\|-		\|-
	\| [[#hth\|~~Helix-turn-helix~~]]		\| [[#hth\|Helixturnhelix]]
	\| Detection of helix-turn-helix nucleic acid binding motifs in proteins		\| Detection of helix-turn-helix nucleic acid binding motifs in proteins
	\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-40CRS27-G&_coverDate=06%2F01%2F2000&_alid=223069367&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5183&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=fcef5227189fa9f0d87d36eeb435c121 EMBOSS]		\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-40CRS27-G&_coverDate=06%2F01%2F2000&_alid=223069367&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5183&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=fcef5227189fa9f0d87d36eeb435c121 EMBOSS]
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	SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences. Information about it can be found [http://www.cbs.dtu.dk/services/SignalP/ here]. The tool is not freely available therefore you have to send a request to the author in order to receive it.		SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences. Information about it can be found [http://www.cbs.dtu.dk/services/SignalP/ here]. The tool is not freely available therefore you have to send a request to the author in order to receive it.

	<span id="~~tmhmm~~"></span>		<span id="hth"></span>

	== ~~TMHMM~~ ==		== Helixturnhelix ==

	~~TMHMM predicts transmembrane regions~~ of proteins. ~~Information about it can be found~~ [http://www.~~cbs~~.~~dtu~~.dk/~~services~~/~~TMHMM~~/ ~~here~~]~~. The tool is not freely available; you have to send a request to the author~~.		Helixturnhelix is part of the EMBOSS package and finds helix-turn-helix nucleic acid binding motifs in proteins.

			To use Helixturnhelix in GenDB you need to install the EMBOSS package from the MRC [http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/download.html download site].

imported>LutzKrause at 16:50, 23 November 2004

2004-11-23T16:50:18Z

← Older revision		Revision as of 18:50, 23 November 2004
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	\| Search for transmembrane regions of proteins		\| Search for transmembrane regions of proteins
	\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11152613&itool=iconabstr TMHMM]		\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11152613&itool=iconabstr TMHMM]
			\|-
			\| [[#hth\|Helix-turn-helix]]
			\| Detection of helix-turn-helix nucleic acid binding motifs in proteins
			\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-40CRS27-G&_coverDate=06%2F01%2F2000&_alid=223069367&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=5183&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=fcef5227189fa9f0d87d36eeb435c121 EMBOSS]
	\|}		\|}

imported>LutzKrause at 14:34, 23 November 2004

2004-11-23T14:34:22Z

← Older revision		Revision as of 16:34, 23 November 2004
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	of family member sequences. The main application of Pfam in GenDB is to predict the domain organization of proteins.		of family member sequences. The main application of Pfam in GenDB is to predict the domain organization of proteins.

	To use Pfam within GenDB you have to install the [http://hmmer.wustl.edu/#download HMMER] package and to download the Pfam database (Pfam_ls.gz) from the [ftp://ftp.sanger.ac.uk/pub/databases/Pfam/ sanger ~~download~~ site].		To use Pfam within GenDB you have to install the [http://hmmer.wustl.edu/#download HMMER] package and to download the Pfam database (Pfam_ls.gz) from the [ftp://ftp.sanger.ac.uk/pub/databases/Pfam/ sanger site].

	=== TIGRFAM database ===		=== TIGRFAM database ===

imported>LutzKrause at 14:33, 23 November 2004

2004-11-23T14:33:04Z

← Older revision		Revision as of 16:33, 23 November 2004
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	= Tools for function prediction integrated in GenDB =		= Tools for function prediction integrated in GenDB =

	In this section tools are described that can be used to predict the function of functional DNA regions like protein coding genes (CDS) within the GenDB annotation system.		In this section tools are described that can be used to predict the function of functional DNA regions like protein coding genes (CDS) within the GenDB annotation system. These tools are autmatically configured by the installation
			system.

	== Currently integrated programs ==		== Currently integrated programs ==
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	\| [[#signalp\|SignalP]]		\| [[#signalp\|SignalP]]
	\| Detection of signal peptide cleavage sites in proteins		\| Detection of signal peptide cleavage sites in proteins
	\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4CKBS0M-3&_coverDate=07%2F16%2F2004&_alid=222995838&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6899&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=d6cec1333e0b2b1aa2d190ff62d26e01 ~~SinalP~~]		\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4CKBS0M-3&_coverDate=07%2F16%2F2004&_alid=222995838&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6899&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=d6cec1333e0b2b1aa2d190ff62d26e01 SignalP]
	\|-		\|-
	\| [[#tmhmm\|TMHMM]]		\| [[#tmhmm\|TMHMM]]
	\| Search for transmembrane regions of proteins		\| Search for transmembrane regions of proteins
	\|		\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11152613&itool=iconabstr TMHMM]
	\|}		\|}

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	TMHMM predicts transmembrane regions of proteins. Information about it can be found [http://www.cbs.dtu.dk/services/TMHMM/ here]. The tool is not freely available; you have to send a request to the author.		TMHMM predicts transmembrane regions of proteins. Information about it can be found [http://www.cbs.dtu.dk/services/TMHMM/ here]. The tool is not freely available; you have to send a request to the author.

	~~Configuring GenDB to support TMHMM is done by the installer. Individual tool instances of TMHMM can be created by using the Tool Creator Wizard or the Tool Configuration Wizard.~~

imported>LutzKrause at 14:29, 23 November 2004

2004-11-23T14:29:32Z

← Older revision		Revision as of 16:29, 23 November 2004
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	\|-		\|-
	\| [[#signalp\|SignalP]]		\| [[#signalp\|SignalP]]
	\| Detection of signal ~~peptides~~		\| Detection of signal peptide cleavage sites in proteins
	\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4CKBS0M-3&_coverDate=07%2F16%2F2004&_alid=222995838&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6899&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=d6cec1333e0b2b1aa2d190ff62d26e01 SinalP]		\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4CKBS0M-3&_coverDate=07%2F16%2F2004&_alid=222995838&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6899&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=d6cec1333e0b2b1aa2d190ff62d26e01 SinalP]
	\|-		\|-
	\| [[#~~sfr~~\|~~SearchforRNAs~~]]		\| [[#tmhmm\|TMHMM]]
	\| ~~Prediction~~ of ~~t- and rRNAs~~		\| Search for transmembrane regions of proteins
	~~\| (Niels Larsen, University Aarhus, Denmark)~~		\|
	\|-
	~~\| [[#trnascan\|tRNAscan-SE]]~~
	\| ~~Prediction of tRNAs~~
	~~\| (http://nar.oupjournals.org/cgi/content/full/25/5/955)~~
	\|-
	~~\| [[#getorf\|Getorf]]~~
	\| ~~Lists all ORFs~~
	~~\| (Contained in EMBOSS package, http://www.hgmp.mrc.ac.uk/Software/EMBOSS/)~~
	\|}		\|}

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	=== HMMFETCH ===		=== HMMFETCH ===
	Instead of fetching single entries from a nSRS server, the HMMER package provides a tool called ''hmmfetch'', which extracts single HMMs from the HMM file. This tool is used similar to the BioPerl indices described above for recomputing the full Pfam result.		Instead of fetching single entries from a nSRS server, the HMMER package provides a tool called ''hmmfetch'', which extracts single HMMs from the HMM file. This tool is used similar to the BioPerl indices described above for recomputing the full Pfam result.

			<span id="interpro"></span>

	== [[InterPro]] ==		== [[InterPro]] ==
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	Setting up InterPRO-Scan is beyond the scope of this documentation. Refer to the included README and FAQ.		Setting up InterPRO-Scan is beyond the scope of this documentation. Refer to the included README and FAQ.

			<span id="sinalp"></span>

	== SignalP ==		== SignalP ==
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	SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences. Information about it can be found [http://www.cbs.dtu.dk/services/SignalP/ here]. The tool is not freely available therefore you have to send a request to the author in order to receive it.		SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences. Information about it can be found [http://www.cbs.dtu.dk/services/SignalP/ here]. The tool is not freely available therefore you have to send a request to the author in order to receive it.

	~~Configuring GenDB to support SignalP is done by the installer. Individual tool instances of SignalP can be created by using the Tool Creator Wizard or the Tool Configuration Wizard.~~		<span id="tmhmm"></span>

	== TMHMM ==		== TMHMM ==

imported>LutzKrause at 14:18, 23 November 2004

2004-11-23T14:18:05Z

← Older revision		Revision as of 16:18, 23 November 2004
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	\| (http://nar.oupjournals.org/cgi/content/full/31/1/315)		\| (http://nar.oupjournals.org/cgi/content/full/31/1/315)
	\|-		\|-
	\| [[#~~rbsfinder~~\|~~RBSFinder~~]]		\| [[#signalp\|SignalP]]
	\| ~~Relocation~~ of ~~CDS starts, Prediction of RBSs~~		\| Detection of signal peptides
	\| (http://~~bioinformatics~~.~~oupjournals~~.~~org~~/~~cgi/reprint/17/12/1123)~~		\| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4CKBS0M-3&_coverDate=07%2F16%2F2004&_alid=222995838&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6899&_sort=d&view=c&_acct=C000057302&_version=1&_urlVersion=0&_userid=2459438&md5=d6cec1333e0b2b1aa2d190ff62d26e01 SinalP]
	\|-		\|-
	\| [[#sfr\|SearchforRNAs]]		\| [[#sfr\|SearchforRNAs]]