firestar-batch Online Help

Functional residues are highly conserved, even across large evolutionary distances. Since these residues are unlikely to have arisen by chance we can use this to help determine the principal isoform. firestar predicts functionally important residues based on the fireDB database. The predictions are based on the local evaluation of alignments between the query sequence and the structures with functional information that are stored in fireDB.

firestar were developed as web service that predicts only ligand binding residues and a confidence score for each residue. At present this web service plays an important role as part of the APPRIS pipeline to annotate splice variants as part of the ENCODE project and, in particular, within GENCODE project.

firestar as a web service

firestar BioMOBY services were designed to be integrated into BioMOBY world, so they generate native MOBY objects with all the information. BioMOBY is an Open Source research project which aims to generate an architecture for the discovery and distribution of biological data through web services. Through a client (ie, Taverna), we will be able to interact with multiple sources of biological data regardless of the underlying format or schema. Data and services are decentralized, but the availability of these resources, and the instructions for interacting with them, are registered in a central location (BioMOBY Central).

BioMOBY paradigm uses a central repository where services are registered. These services have been registered in INB Central repository:

BioMOBY services can be used into workflows using the Taverna (http://taverna.sourceforge.net/) client, where if you want to download Scufle file, click here.

BioMOBY Input

	<moby:FASTA_AA_multi moby:namespace="" moby:id="query">
		<moby:String moby:namespace="" moby:id="" moby:articleName="SequenceString">
		>2JK5_1
		QVQLQQPGAELVKPGASVKLSCKASGYTFTSDWIHWVKQRPGHGLEWIGEIIPSYGRANYNEKIQKKATLTADKSSSTAFMQLSSLTSEDSAVYYCARERGDGYFAVWGAGTTVTVSSA
		KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSSWPSETVTCNVAHPASSTKVDKKIVPRD
		>2JK5_3
		MPPMLSGLLARLVKLLLGRHGSALHWRAAGAATVLLVIVLLAGSYLAVLAERGAPGAQLITYPRALWWSVETATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALATWFVGREQ
		ERRGH
		>2JK5_2
		DILLTQSPAILSVSPGERVSFSCRASQSIGTDIHWYQQRTNGSPRLLIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIANYYCQQSNRWPFTFGSGTKLEIKRADAAPTVSIFP
		PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN
		>2JKY_1
		SANDKQYISYNNVHQLCQVSAERIKNFKPDLIIAIGGGGFIPARILRTFLKEPGVPTIRIFAIILSLYEDLNSVGSEVEEVGVKVSRTQWIDYEQCKLDLVGKNVLIVDEVDDTRTTLH
		YALSELEKDAAEQAKAKGIDTEKSPEMKTNFGIFVLHDKQKPKKADLPAEMLNDKNRYFAAKTVPDKWYAYPWESTDIVFHTRMAIEQGNDIFI
		</moby:String>
	</moby:FASTA_AA_multi>
	

BioMOBY Output

	<moby:Firestar_Text namespace="" id="" articleName="">
		<moby:String namespace="" id="" articleName="content"><![CDATA[
		/*
		 * firestar
		 *   prediction of functionally important residues using structural templates and alignment reliability.
		 * Gonzalo Lopez; A. Valencia; M. Tress Nucleic Acids Research, doi:10.1093/nar/gkm297
		 * Date: Jan 1, 2011
		 */
		
		# ============================================ #
		# Functional residues and structural templates #
		# ============================================ #
		######
		50      6       GLEWIGEIIPSYG    1m71B
		59      5       PSYGRANYNEKIQ    1m71B
		>>>     2JK5_1  2       50,59
		######
		40      4       VLLVIVLLAGSYL    2zd9C
		66      5       ITYPRALWWSVET    2zd9C
		70      6       RALWWSVETATTV    2zd9C
		76      6       VETATTVGYGDLY    2h8pC  1k4cC  2r9rH  2ahzA  2ih3C  3jycA  2qksA  2ahzA  3jycA  2zd9C  2h8pC  2a79B  1k4cC  2r9rH  2a79B  2qksA  2h8pC
		81      6       TVGYGDLYPVTLW    1xl6A
		86      6       DLYPVTLWGRCVA    1k4cC  2ih3C  2h8pD
		89      6       PVTLWGRCVAVVV    1k4cC  2ih3C  2h8pD
		93      6       WGRCVAVVVMVAG    1k4cC  2h8pD
		>>>     2JK5_3  8       40,66,70,76,81,86,89,93
		######
		35      5       PDLIIAIGGGGFI    1a95C
		38      6       IIAIGGGGFIPAR    1a95C
		68      6       AIILSLYEDLNSV    2jkyA
		84      6       VEEVGVKVSRTQW    2jkyA
		109     6       KNVLIVDEVDDTR    1a95C  2jkyA
		113     6       IVDEVDDTRTTLH    2jkyA
		117     6       VDDTRTTLHYALS    2jkyA
		158     6       IFVLHDKQKPKKA    2jkyA
		187     6       KTVPDKWYAYPWE    2jkyA
		190     6       PDKWYAYPWESTD    2jkyA
		193     6       WYAYPWESTDIVF    2jkyA
		>>>     2JKY_1  11      35,38,68,84,109,113,117,158,187,190,193
		######
		96      6       QSNRWPFTFGSGT    1c12A
		138     6       VVCFLNNFYPKDI    2uylA  3hc0B  3eyvA  1t4kA  3f12C  2qscL
		151     6       NVKWKIDGSERQN    1kn2L  2uylA  1cicC  1mnuL  2v17L  1t4kA  3hc0B  2i9lA
		167     6       NSWTDQDSKDSTY    2uylA  1t4kA
		185     6       LTLTKDEYERHNS    1a3lL  1t4kA  1mamL  2i9lA  1q9kA  2ajsL  2oz4L
		188     6       TKDEYERHNSYTC    2i9lA
		>>>     2JK5_2  6       96,138,151,167,185,188
		
		# ============================== #
		# Prediction of consensus motifs #
		# ============================== #
		######
		C>>     2JK5_1
		######
		C>>     2JK5_3
		######
		C>>     2JKY_1
		######
		C>>     2JK5_2
		]]></moby:String>
	</moby:Firestar_Text>
	

Perl program example

A Perl program example, running_runFirestar.pl about invoking and parsing firestar BioMOBY web services. It uses the following libraries:

To run this script:

running_runFirestar.pl
		
	--input= <Amino acid sequences file as FASTA format>

	--output= <Output file where firestar reponses will be saved>
		

Using this input sample, you will run the script as below:

running_runFirestar.pl --input=sample.faa --output=sample.output

CNIO / INB