M_Fetch_e-T_phylo_boot - (BETA)

Created: 2010-03-10 15:44:02 Last updated: 2010-03-10 15:49:06

Download Workflow

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.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/1097/download?version=1
[ More Info Expand ]

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 Uploader

Achille Zappa

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (2)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (12)

Uploader tags

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

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

2209 viewings

1653 downloads

[ see breakdown ]

Citations (0)Version History

None

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

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

Uploader

Achille Zappa

Workflow for Automated Comparative Protein... (2)

Download

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.

Created: 2010-06-29 | Last updated: 2010-08-31

Credits: Achille Zappa

Attributions: EBI_ClustalW_alignment_tree

Taverna 1

Uploader

Achille Zappa

MY_Multi_Alignment_Phylo (1)

Download

This workflow performs a 'multiple' multiple sequence alignment and phylogenetic analysis.

Created: 2009-11-03

Credits: Achille Zappa