Workflow for Protein Sequence Analysis

Created: 2008-01-09 12:03:03 Last updated: 2008-01-09 12:31:27

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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
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

Beanshells (9)

Name	Inputs	Outputs
Condition_Protein	sequence	condition
toLowerCase	input	output
extract_number_sequences	insertSeq	result
Extract_Duplicates	BlastList UserList	result
insert_query_seq	fasta MergeString	result
Extract_GI_Evalue	BlastReport	result
Setting_fasta	sequence	fasta
Extract_Seq_Description	Sequences	result
Condition_DNA_RNA	sequence	condition

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)

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

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

Information Workflow Type

Taverna 1

Information Uploader

M.B.Mon...

Information License

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Information Version 1 (of 1)

Information Credits (1)

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M.B.Monteiro

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AbuJarour

Information Statistics

10219 viewings

7519 downloads

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Version History

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Workflow for Protein Sequence Analysis

Created by M.B.Monteiro on Wednesday 09 January 2008 12:03:03 (UTC)

Last edited by M.B.Monteiro on Wednesday 09 January 2008 12:31:27 (UTC)

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