Workflow for Automated Comparative Protein Sequences Analysis

None

/* Accepts sequences in FASTA format and extracts the information from them for a better understanding of the multiple sequence alignment and trees plots. It uses regular expression for the extraction
Input: Sequences; 
Output: result; string with description of each sequence in FASTA format
*/

// Extract the FASTA description from each sequence
import java.util.regex.Pattern;
import java.util.regex.Matcher;

StringBuffer temp = new StringBuffer();
String information="";
// regular expression to extract only the sequence description
Pattern pattern = Pattern.compile (">(\\w+.*)\\s");
Matcher matcher = pattern.matcher(Sequences);

while(matcher.find()){
	information=matcher.group(1);
	temp.append(information + "\n");
}

// Output sequence description
String result = temp.toString();

Name	Type	Description
Fetch	workflow
T_coffee	workflow
Muscle	workflow
ClustalW2	workflow
emma	soaplab	Endpoint http://www.ebi.ac.uk/soaplab/services/alignment_multiple.emma
emma_sprotein_seq	stringconstant	Value Yes
emma_osformat_outseq	stringconstant	Value clustal
email	stringconstant	Value achille.zappa@istge.it
database	stringconstant	Value uniprot
ML_reps	stringconstant	Value 3
NJ_reps	stringconstant	Value 50
MAFFT	workflow
ClustalW2_ML	workflow
ClustalW2_NJ	workflow
Muscle_ML	workflow
Muscle_NJ	workflow
emma_ML	workflow
emma_NJ	workflow
Tcoffee_ML	workflow
Tcoffee_NJ	workflow
MAFFT_ML	workflow
MAFFT_NJ	workflow
Beanshell	beanshell	Script /* Accepts sequences in FASTA format and extracts the information from them for a better understanding of the multiple sequence alignment and trees plots. It uses regular expression for the extraction Input: Sequences; Output: result; string with description of each sequence in FASTA format / // Extract the FASTA description from each sequence import java.util.regex.Pattern; import java.util.regex.Matcher; StringBuffer temp = new StringBuffer(); String information=""; // regular expression to extract only the sequence description Pattern pattern = Pattern.compile (">(\\w+.)\\s"); Matcher matcher = pattern.matcher(Sequences); while(matcher.find()){ information=matcher.group(1); temp.append(information + "\n"); } // Output sequence description String result = temp.toString();

Name	Inputs	Outputs
Beanshell	Sequences	result
Beanshell	inputs	result
Beanshell_2	inputs	result
Beanshell_3	inputs	result
Beanshell_2_2	inputs	result
Beanshell_4	inputs	result
Beanshell_2_3	inputs	result
Beanshell_5	inputs	result
Beanshell_2_4	inputs	result
Beanshell	inputs	result
Beanshell_2	inputs	result
Beanshell_3	inputs	result
Beanshell_2_2	inputs	result
Beanshell_4	inputs	result
Beanshell_2_3	inputs	result
Beanshell_5	inputs	result
Beanshell_2_4	inputs	result
Beanshell	inputs	result
Beanshell_2	inputs	result
Beanshell_3	inputs	result
Beanshell_2_2	inputs	result
Beanshell_4	inputs	result
Beanshell_2_3	inputs	result
Beanshell_5	inputs	result
Beanshell_2_4	inputs	result
Beanshell	inputs	result
Beanshell_2	inputs	result
Beanshell_3	inputs	result
Beanshell_2_2	inputs	result
Beanshell_4	inputs	result
Beanshell_2_3	inputs	result
Beanshell	inputs	result
Beanshell_2	inputs	result
Beanshell_3	inputs	result
Beanshell_2_2	inputs	result
Beanshell_4	inputs	result
Beanshell_2_3	inputs	result
Beanshell	inputs	result
Beanshell_2	inputs	result
Beanshell_3	inputs	result
Beanshell_2_2	inputs	result
Beanshell_4	inputs	result
Beanshell_2_3	inputs	result
Beanshell	inputs	result
Beanshell_2	inputs	result
Beanshell_3	inputs	result
Beanshell_2_2	inputs	result
Beanshell_4	inputs	result
Beanshell_2_3	inputs	result
Beanshell	inputs	result
Beanshell_2	inputs	result
Beanshell_3	inputs	result
Beanshell_2_2	inputs	result
Beanshell_4	inputs	result
Beanshell_2_3	inputs	result
Beanshell_5	inputs	result
Beanshell_2_4	inputs	result
Beanshell	inputs	result
Beanshell_2	inputs	result
Beanshell_3	inputs	result
Beanshell_2_2	inputs	result
Beanshell_4	inputs	result
Beanshell_2_3	inputs	result
Beanshell_5	inputs	result
Beanshell_2_4	inputs	result
Beanshell	inputs	result
Beanshell_2	inputs	result
Beanshell_3	inputs	result
Beanshell_2_2	inputs	result
Beanshell_4	inputs	result
Beanshell_2_3	inputs	result

Name	Description
seqs
o
t1
emmaln
3
4
5
6
7
8
q
w
e
y
u
i
mm
W2-1
W2-2
W2-3
W2-4
W2-5
W2-6
W2-7
W2-8
W2-O
W2-aln
W2-nj
W2-t
TCoffee_aln
TCoffee_dnd
MAFFT_out
desc

Source	Sink
seqs_ids	Fetch:Sequences_or_IDs
database:value	Fetch:DB
emma:outseq	T_coffee:Sequences
email:value	T_coffee:email
Fetch:sequences	Muscle:Sequences
email:value	Muscle:email
Fetch:sequences	ClustalW2:Sequences
email:value	ClustalW2:Email_address
emma_sprotein_seq:value	emma:sprotein_sequence
emma_osformat_outseq:value	emma:osformat_outseq
Fetch:sequences	emma:sequence_direct_data
Fetch:sequences	MAFFT:s
ClustalW2:ClustalW2_alignment	ClustalW2_ML:s
ML_reps:value	ClustalW2_ML:r
ClustalW2:ClustalW2_alignment	ClustalW2_NJ:in
NJ_reps:value	ClustalW2_NJ:r
Muscle:MUSCLE_alignment	Muscle_ML:s
ML_reps:value	Muscle_ML:r
Muscle:MUSCLE_alignment	Muscle_NJ:in
NJ_reps:value	Muscle_NJ:r
emma:outseq	emma_ML:s
ML_reps:value	emma_ML:r
emma:outseq	emma_NJ:in
NJ_reps:value	emma_NJ:r
T_coffee:TCoffee_aln	Tcoffee_ML:s
ML_reps:value	Tcoffee_ML:r
T_coffee:TCoffee_aln	Tcoffee_NJ:in
NJ_reps:value	Tcoffee_NJ:r
MAFFT:s	MAFFT_ML:s
ML_reps:value	MAFFT_ML:r
MAFFT:s	MAFFT_NJ:in
NJ_reps:value	MAFFT_NJ:r
Fetch:sequences	Beanshell:Sequences
Fetch:sequences	seqs
emma:dendoutfile	o
T_coffee:TCoffee_alignment	t1
emma:outseq	emmaln
emma_NJ:out	3
emma_NJ:outree	4
emma_ML:out	5
emma_ML:outree	6
ClustalW2_ML:out	7
ClustalW2_ML:outree	8
ClustalW2_NJ:out	q
ClustalW2_NJ:outree	w
Tcoffee_ML:out	e
Tcoffee_ML:outree	y
Tcoffee_NJ:out	u
Tcoffee_NJ:outree	i
Muscle:MUSCLE_alignment	mm
Muscle_NJ:out	W2-1
Muscle_NJ:outree	W2-2
Muscle_ML:out	W2-3
Muscle_ML:outree	W2-4
MAFFT_NJ:out	W2-5
MAFFT_NJ:outree	W2-6
MAFFT_ML:out	W2-7
MAFFT_ML:outree	W2-8
ClustalW2:ClustalW2_output	W2-O
ClustalW2:ClustalW2_alignment	W2-aln
ClustalW2:ClustalW2_nj_tree	W2-nj
ClustalW2:ClustalW2_phylip_tree	W2-t
T_coffee:TCoffee_aln	TCoffee_aln
T_coffee:TCoffee_dnd	TCoffee_dnd
MAFFT:s	MAFFT_out
Beanshell:result	desc

Workflow for Automated Comparative Protein Sequences Analysis

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Endpoint

Value

Value

Value

Value

Value

Value

Script

Reviews (0)

Comments (0)

Other workflows that use similar services (24)