Workflow Entry: Workflow for Protein Sequence Analysis

Created at: 09/01/08 @ 12:03:04 Last updated: 09/01/08 @ 12:31:29

Version 1 (of 1)

Version created on: 09/01/08 @ 12:03:03 by: M.B.Monteiro | Revision comments Expand

Last edited on: 09/01/08 @ 12:31:27 by: M.B.Monteiro

Title: Workflow for Protein Sequence Analysis

Type: Taverna 1

Preview

(Click on the image to get the full size)

Workflow_for_protein_sequence_analysis_5539_1

Download Scalable Diagram (SVG)

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.

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/124/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (3)

Name	Description
Input_Sequence	Enter a novel protein sequence. e.g. AITRRVACLDGVNTATNAACCALFAVRDDIQQNL FDGGECGEEVHESLRLTFHDAIGISPSLAATGKFGG GGADGSIMIFDDIEPNFHANNGVDEIINAQKPFVAK HNMTAGDFIQFAGAVGVSNCPGAPQLSFFLGRPA
ListUser	Enter a list of protein IDs. e.g: Q96TS5 Q12575 AAA33739 Q96TS6 AAA33741
N-J or UPGMA	For the cluster method enter "n" for Neighbor-Joining algorithm or "u" for UPGMA algorithm

Processors (28)

Name	Type	Description
Fail_if_false_DNA	local
Fail_if_false_Protein	local
Not_Protein_Sequence	stringconstant
Get_Protein_FASTA	local
Is_DNA_RNA	stringconstant
Fail_if_true_Protein	local
FlattenImage	local
Fail_if_true_DNA	local
Split_by_newline	local
MergeString	local
MergeUserList	local
Condition_Protein	beanshell
toLowerCase	beanshell
extract_number_sequences	beanshell
Extract_Duplicates	beanshell
insert_query_seq	beanshell
Extract_GI_Evalue	beanshell
Setting_fasta	beanshell
Extract_Seq_Description	beanshell
Condition_DNA_RNA	beanshell
blastsimplifier	soaplabwsdl	Simplifies BLAST output for later use
fdrawgram	soaplabwsdl	Plots a cladogram- or phenogram-like rooted tree diagram
fprotdist	soaplabwsdl	Protein distance algorithm
fneighbor	soaplabwsdl	Phylogenies from distance matrix by N-J or UPGMA method
fdrawtree	soaplabwsdl	Plots an unrooted tree diagram
prettyplot	soaplabwsdl	Displays aligned sequences, with colouring and boxing
ClustalW	soaplabwsdl	Multiple alignment program - interface to ClustalW program
searchSimple	arbitrarywsdl	Execute Blast

Outputs (9)

Name	Description
Blast Report
Protein Description
Image Alignment
Output Tree (N or UPGMA)
Distance Outfile
Rooted_Tree
Unrooted_Tree
Not Protein Sequence
It is a DNA or RNA sequence

Links (38)

Sink	Source
fprotdist:sequence_direct_data	ClustalW:outseq
prettyplot:sequences_direct_data	ClustalW:outseq
Fail_if_false_Protein:test	Condition_Protein:condition
Fail_if_true_Protein:test	Condition_Protein:condition
Split_by_newline:string	Extract_Duplicates:result
Extract_Duplicates:BlastList	Extract_GI_Evalue:result
Condition_DNA_RNA:sequence	Input_Sequence
Condition_Protein:sequence	Input_Sequence
Setting_fasta:sequence	Input_Sequence
MergeUserList:stringlist	ListUser
Fail_if_false_DNA:test	Condition_DNA_RNA:condition
Fail_if_true_DNA:test	Condition_DNA_RNA:condition
MergeString:stringlist	Get_Protein_FASTA:outputText
insert_query_seq:MergeString	MergeString:concatenated
Extract_Duplicates:UserList	MergeUserList:concatenated
toLowerCase:input	N-J or UPGMA
insert_query_seq:fasta	Setting_fasta:fasta
searchSimple:query	Setting_fasta:fasta
Get_Protein_FASTA:id	Split_by_newline:split
Extract_GI_Evalue:BlastReport	blastsimplifier:output
ClustalW:sequence_direct_data	extract_number_sequences:result
Extract_Seq_Description:Sequences	extract_number_sequences:result
Protein Description	Extract_Seq_Description:result
Image Alignment	FlattenImage:outputlist
It is a DNA or RNA sequence	Is_DNA_RNA:value
Not Protein Sequence	Not_Protein_Sequence:value
Rooted_Tree	fdrawgram:plotfile
Unrooted_Tree	fdrawtree:plotfile
Distance Outfile	fneighbor:outfile
Output Tree (N or UPGMA)	fneighbor:outtreefile
fdrawgram:intreefile_direct_data	fneighbor:outtreefile
fdrawtree:intreefile_direct_data	fneighbor:outtreefile
fneighbor:datafile_direct_data	fprotdist:outfile
extract_number_sequences:insertSeq	insert_query_seq:result
FlattenImage:inputlist	prettyplot:Graphics_in_PNG
Blast Report	searchSimple:Result
blastsimplifier:new_direct_data	searchSimple:Result
fneighbor:treetype	toLowerCase:output

Coordinations (6)

Controller	Target
Fail_if_true_Protein	Not_Protein_Sequence
Fail_if_false_Protein	Setting_fasta
Fail_if_true_DNA	Condition_Protein
Fail_if_false_DNA	Is_DNA_RNA
Fail_if_false_Protein	MergeUserList
Fail_if_false_Protein	toLowerCase