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M_Fetch_e-T_phylo_boot - (BETA)

Workflow Entry: M_Fetch_e-T_phylo_boot - (BETA)

Created at: 10/03/10 @ 15:44:02 Last updated: 10/03/10 @ 15:49:06

Version 1 (of 1)

Version created on: 10/03/10 @ 15:44:02 by: Achille Zappa | Revision comments Expand

Last edited on: 10/03/10 @ 15:49:13 by: Achille Zappa

Title: M_Fetch_e-T_phylo_boot - (BETA)

Type: Taverna 1

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Description

This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.

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Workflow Components

Inputs (3)

Name	Description
seq_ids
db
email

Processors (16)

Name	Type	Description
String_Constant	stringconstant
String_Constant1	stringconstant
seq_descriptions	beanshell
Muscle	workflow	Perform a multiple sequence alignment using the MUSCLE tool (see http://www.drive5.com/muscle/). The EBI's WSMuscle web service (see http://www.ebi.ac.uk/Tools/webservices/services/muscle) is used.
Fetch	workflow	Given a sequence or sequence entry identifer (e.g. uniprot:wap_rat), return the sequence in fasta format. If a sequence identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the sequence in fasta format. Otherwise the input is assumed to be a sequence and if passed through the Soaplab EMBOSS seqret service to force the sequence into fasta format.
T_coffee	workflow	Perform a multiple sequence alignment using T-Coffee (see http://www.tcoffee.org/). The EBI's WSToffee web service (see http://www.ebi.ac.uk/Tools/webservices/services/tcoffee) ise used.
ClustalW2	workflow	Given a set of sequences perform an multiple sequence alignment and from the multiple alignment derive a phylogenetic tree. The popular ClustalW program (see http://www.clustal.org/), as implemented in the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) is used to perform both tasks.
emma	soaplabwsdl	Multiple sequence alignment (ClustalW wrapper)
emma_ML	workflow
Muscle_NJ	workflow
T_coffe_ML	workflow
ClustalW2_NJ	workflow
ClustalW2_ML	workflow
Muscle_ML	workflow
T_coffee_NJ	workflow
emma_NJ	workflow

Beanshells (7)

Name	Description	Inputs	Outputs
Is_done	Convert status code into true/false.	job_status	is_done
sequences		in	out
Is_sequence	Return true if the input is a sequence or false if the input is a sequence identifer (e.g. uniprot:wap_rat).	sequence	is_sequence
Is_done	Map job status to true/false	job_status	is_done
Is_done	Map job status into true/false is done flag	job_status	is_done
Is_done	Map job status into true/false is done flag	job_status	is_done
seq_descriptions		sequences	result

Outputs (44)

Name	Description
Sequences
CW_t_newick
Tcoffee_aln_1
emma_CW_aln
CW_nj_cons_out
CW_nj_radial_ps
CW_nj_rect_ps
CW_nj_cons_newick
CW_nj_boot_out
CW_ml_cons_out
CW_ml_boot_out
CW_ml_cons_newick
Tc_nj_cons_out
Tc_nj_radial_ps
Tc_nj_rect_ps
Tc_nj_cons_newick
Tc_nj_boot_out
Tc_ml_cons_out
Tc_ml_boot_out
Tc_ml_cons_newick
M_nj_cons_out
M_nj_radial_ps
M_nj_rect_ps
M_nj_cons_newick
M_nj_boot_out
M_ml_cons_out
M_ml_boot_out
M_ml_cons_newick
Muscle_aln
CW2_nj_cons_out
CW2_nj_radial_ps
CW2_nj_rect_ps
CW2_nj_cons_newick
CW2_nj_boot_out
CW2_ml_cons_out
CW2_ml_boot_out
CW2_ml_cons_newick
CW2_Out
CW2_aln
CW2_nj_rep
CW2_t_newick
TCoffee_aln
TCoffee_newick
seq_descs

Links (70)

Source	Sink
ClustalW2:ClustalW2_alignment	ClustalW2_ML:i
ClustalW2:ClustalW2_alignment	ClustalW2_NJ:i
Fetch:sequences	emma:sequence_direct_data
Fetch:sequences	seq_descriptions:sequences
Muscle:MUSCLE_alignment	Muscle_ML:i
Muscle:MUSCLE_alignment	Muscle_NJ:i
String_Constant1:value	Muscle_NJ:reps
T_coffee:TCoffee_alignment	T_coffe_ML:i
T_coffee:TCoffee_alignment	T_coffee_NJ:i
db	Fetch:DB
email	ClustalW2:Email_address
email	Muscle:email
email	T_coffee:email
emma:outseq	T_coffee:Sequences
emma:outseq	emma_ML:i
emma:outseq	emma_NJ:i
seq_ids	Fetch:Sequences_or_IDs
ClustalW2:ClustalW2_alignment	CW2_aln
ClustalW2:ClustalW2_nj_tree	CW2_nj_rep
ClustalW2:ClustalW2_output	CW2_Out
ClustalW2:ClustalW2_phylip_tree	CW2_t_newick
ClustalW2_ML:a	CW2_ml_boot_out
ClustalW2_ML:o	CW2_ml_cons_out
ClustalW2_ML:o2	CW2_ml_cons_newick
ClustalW2_NJ:o1	CW2_nj_cons_out
ClustalW2_NJ:o2	CW2_nj_radial_ps
ClustalW2_NJ:o3	CW2_nj_rect_ps
ClustalW2_NJ:o4	CW2_nj_cons_newick
ClustalW2_NJ:o5	CW2_nj_boot_out
Fetch:sequences	ClustalW2:Sequences
Fetch:sequences	Muscle:Sequences
Fetch:sequences	Sequences
Muscle:MUSCLE_alignment	Muscle_aln
Muscle_ML:a	M_ml_boot_out
Muscle_ML:o	M_ml_cons_out
Muscle_ML:o2	M_ml_cons_newick
Muscle_NJ:o1	M_nj_cons_out
Muscle_NJ:o2	M_nj_radial_ps
Muscle_NJ:o3	M_nj_rect_ps
Muscle_NJ:o4	M_nj_cons_newick
Muscle_NJ:o5	M_nj_boot_out
String_Constant1:value	ClustalW2_NJ:reps
String_Constant1:value	T_coffee_NJ:reps
String_Constant1:value	emma_NJ:reps
String_Constant:value	ClustalW2_ML:reps
String_Constant:value	Muscle_ML:reps
String_Constant:value	T_coffe_ML:reps
String_Constant:value	emma_ML:reps
T_coffe_ML:a	Tc_ml_boot_out
T_coffe_ML:o	Tc_ml_cons_out
T_coffe_ML:o2	Tc_ml_cons_newick
T_coffee:TCoffee_alignment	TCoffee_aln
T_coffee:TCoffee_aln	Tcoffee_aln_1
T_coffee:TCoffee_dnd	TCoffee_newick
T_coffee_NJ:o1	Tc_nj_cons_out
T_coffee_NJ:o2	Tc_nj_radial_ps
T_coffee_NJ:o3	Tc_nj_rect_ps
T_coffee_NJ:o4	Tc_nj_cons_newick
T_coffee_NJ:o5	Tc_nj_boot_out
emma:dendoutfile	CW_t_newick
emma:outseq	emma_CW_aln
emma_ML:a	CW_ml_boot_out
emma_ML:o	CW_ml_cons_out
emma_ML:o2	CW_ml_cons_newick
emma_NJ:o1	CW_nj_cons_out
emma_NJ:o2	CW_nj_radial_ps
emma_NJ:o3	CW_nj_rect_ps
emma_NJ:o4	CW_nj_cons_newick
emma_NJ:o5	CW_nj_boot_out
seq_descriptions:result	seq_descs

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Achille Zappa

Information License

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Information Credits (2)

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Information Attributions (0)

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None

Information Tags (12)

Original Uploader tags

alignment
|
analysis
|
clustal
|
consensus
|
fetch
|
ml
|
muscle
|
nj
|
phylogeny
|
protein
|
sequence
|
tree

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Information Favourited By (0)

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Information Statistics

467 viewings

347 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - M_Fetch_e-T_phylo_boot - (BETA)

Created on: Wednesday 10 March 2010 @ 15:44:02 (GMT)

Created by: Achille Zappa

Last edited on: Wednesday 10 March 2010 @ 15:49:13 (GMT)

Last edited by: Achille Zappa

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Other workflows that use similar services (24)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 2

Original Uploader

Achille Zappa

Workflow for Automated Comparative Protein Sequences Analysis (v2)

Created: 29/06/10 @ 12:59:57 | Last updated: 31/08/10 @ 09:43:41

Credits: Achille Zappa

Attributions: EBI_ClustalW_alignment_tree

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

This workflow performs "parallel" generic protein sequence analysis. In order to do that a list of known protein identifiers chosen by the biologist enters into the software to perform different multiple sequence alignments and finally phylogenetic analysis.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 48 times | Downloaded: 11 times

This Workflow has no tags!