M_Fetch_e-T_phylo_boot - (BETA)
Created: 2010-03-10 15:44:02
Last updated: 2010-03-10 15:49:06
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 |
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