SifterWorkflow_Prod_Neu

Created: 2007-11-23 16:42:24 Last updated: 2008-04-29 10:37:12

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Phylogenomic workflow with SIFTER.

The workflow first runs an iterative Blast search against the RefSeq database (Pruitt et al. 2007) (only fully sequenced organisms) and filters the results to get putative orthologous and in-paralogous proteins. These sequences are used to build a multiple alignment with MAFFT (Katoh et al. 2005). After filtering out alignment columns with more than 60% gaps, a phylogenetic tree is build. If there are less than 20 proteins in the alignment Phyml (Guindon and Gascuel 2003), a maximum likelihood approach, is used. For more than 20 proteins BioNJ (Gascuel et al. 1997), a neighbour joining method, is applied to speed up the pipeline. FORESTER (Zmasek and Eddy 2001) is called to reconcile the tree with the species tree, thereby annotating duplication and speciation nodes. Finally SIFTER is run to transfer Gene Ontology (The Gene Ontology Consortium 2000) terms inside the phylogenetic tree.

Please use as inputs for organism the latin name with upper case letter in front:

e.g. Medicago truncatula

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Workflow Components

Inputs (4)

Name	Description
seq
length
organism
gene_name

Processors (10)

Name	Type	Description
BuildPhylogeneticTreeFromFastaAlignment	biomobywsdl	Builds the most accurate phylogenetic tree. For small trees (< 20 sequences) a maximum likelihood approach (Phyml) and for greater trees a very good and high performance neighbor joining algorithm (BioNJ) is used.
buildMultipleAlignmentWithMAFFT	biomobywsdl	Builds a multiple alignment with MAFFT from a set of fasta files.
GetConservedDomainsFromFastaAlignment	biomobywsdl	Extract conserved regions from fasta alignment.
GetInAndOrthologsFromRefSeq	biomobywsdl	Runs a iterative Blastp searches against the RefSeq database with only full sequenced organisms. Inparalogs and Orthologs are returned in fasta format
organism	biomobyobject	an object
RunSifter	biomobywsdl	SIFTER uses a phylogenomic inference algorithm to transfer Ontology terms inside a phylogenetic tree. The result are GO Terms predicted by SIFTER for the gene with name "gene_name". Please make sure, that "gene_name" is in phylogenetic tree and the other genes in the tree are RefSeqProt proteins!
Integer	biomobyobject	an int
gene_name	biomobyobject	an object
String	biomobyobject	a string
AminoAcidSequence	biomobyobject	Lightweight representation an amino acid sequence

Beanshells (0)

Outputs (9)

Name	Description
mafft
fasta
pli
gos
family
forester
tree
alignment2
scale

Links (25)

Source	Sink
BuildPhylogeneticTreeFromFastaAlignment:Newick_Text(phyogenetic_tree)	RunSifter:Newick_Text(phyogenetic_tree)
Integer:mobyData	AminoAcidSequence:Integer(Length)
String:mobyData	AminoAcidSequence:String(SequenceString)
gene_name	gene_name:id
gene_name:mobyData	GetInAndOrthologsFromRefSeq:Object(gene_name)
gene_name:mobyData	RunSifter:Object(gene_name)
length	Integer:value
organism	organism:id
organism:mobyData	GetInAndOrthologsFromRefSeq:Object(organism)
organism:mobyData	RunSifter:Object(organism)
seq	String:value
AminoAcidSequence:mobyData	GetInAndOrthologsFromRefSeq:AminoAcidSequence(sequence)
GetConservedDomainsFromFastaAlignment:alignment_in_fasta_format(alignment)	BuildPhylogeneticTreeFromFastaAlignment:alignment_in_fasta_format(alignment)
GetConservedDomainsFromFastaAlignment:alignment_in_fasta_format(alignment)	RunSifter:alignment_in_fasta_format(alignment)
GetInAndOrthologsFromRefSeq:FASTA_AA(Collection - 'fasta')	buildMultipleAlignmentWithMAFFT:FASTA_AA(Collection - 'fasta')
buildMultipleAlignmentWithMAFFT:alignment_in_fasta_format(fasta_alignment)	GetConservedDomainsFromFastaAlignment:alignment_in_fasta_format(fasta_alignment)
BuildPhylogeneticTreeFromFastaAlignment:output	tree
GetConservedDomainsFromFastaAlignment:output	alignment2
GetInAndOrthologsFromRefSeq:output	fasta
RunSifter:Annotated_GO_Term_With_Probability(Collection - 'GO_term')	gos
RunSifter:Newick_Text(forester_file)	forester
RunSifter:text-plain(family_file)	family
RunSifter:text-plain(scale_file)	scale
RunSifter:text-xml(pli_file)	pli
buildMultipleAlignmentWithMAFFT:output	mafft

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Information Workflow Type

Taverna 1

Information Uploader

Anika Joecker

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Information Version 2 (latest) (of 2)

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Anika Joecker

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Lipeter1

Information Statistics

7674 viewings

3131 downloads

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Citations (1)

1. B.E. Engelhardt, M.I. Jordan, K.E. Muratore, and S.E. Brenner, Protein molecular function prediction by Bayesian ph\ylogenomics, 07 October 2005

Version History

In chronological order:

SifterWorkflow1

Created by Anika Joecker on Friday 23 November 2007 16:42:24 (UTC)

Last edited by Anika Joecker on Friday 14 December 2007 13:08:46 (UTC)
SifterWorkflow_Prod_Neu

Created by Anika Joecker on Friday 23 November 2007 16:42:24 (UTC)

Last edited by Anika Joecker on Tuesday 29 April 2008 10:37:12 (UTC)

Revision comment:

Change to the new BioMOBY repository at Calgary

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