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LBEEP

@@ -39,7 +39,7 @@ for($i=0;$i<@ARGV;$i++){
 	if($ARGV[$i] eq "-M"){
 		$MODEL = $ARGV[$i+1];
 		$MODEL=~s/\s//g;
-		if(($MODEL ne 'B') && ($MODEL ne 'O')){ print "-M $MODEL invalid option! use 'B' or 'O' Exiting !\n"; exit;}
+		if(($MODEL ne 'B') && ($MODEL ne 'O')&&($MODEL ne 'C')){ print "-M $MODEL invalid option! use 'B' or 'O' or 'C' Exiting !\n"; exit;}
 	}
 	if($ARGV[$i] eq "-t"){
 		$Thresh = $ARGV[$i+1];

README.md

@@ -25,7 +25,8 @@ Linear B-Cell Exact Epitope Predictor
    -i : input file in fasta format (mandatory). 
         Note: The option does not validate the FASTA format and hence make sure the input sequence is in fasta format.
    -m : mode either 'pep' for peptide or 'pro' for protein  (mandatory).
-   -M : Model to be used 'B' for balanced model and 'O' for original model (default Balanced model).
+   -M : Model to be used 'B' for balanced model, 'C' for confirmed model, and 'O' for original model (default Balanced model).
+	For the confirmed model, the dataset constructed in LBtope (LBtope_confirm) was utilizd, where epitopes/non-epitopes were confirmed 		by atleast two experimental studies.
    -t : threshold for predcition; integer ranging between 0.0 and 1.0 (default 0.6).
    -o : output file (if not mentioned output will be stored in LBEEP_out file).
 
@@ -39,14 +40,14 @@ Linear B-Cell Exact Epitope Predictor
 5. Limitations
    ============
 
-   (a) Since the model is trained using epitopes and non-epitopes of length >5 and <=15, prediction made for peptides other than these length will be undesirable. Hence, it is advised not to mention window size less than 6 and > 15 in protein mode.
+   (a) Since the models (Original and Balanced) are trained using epitopes and non-epitopes of length >5 and <=15, predictions made for peptides other than these lengths will be undesirable. Hence, it is advised not to mention window size less than 6 and greater than 15 in protein mode, and not advised to input peptides of length less than 6 and greater than 15 in peptide mode. However, these may not be true in the case of "Confirm" mode.
 
 6. Example
    =======
-
    (a) ./LBEEP -i test_input_peptides -m pep -M B -o Test_peptide 
    (b) ./LBEEP -i test_input_protein -m pro -M B -t 0.6 -o Test_protein
-
+   (c) ./LBEEP -i test_input_peptides -m pep -M C -o Test_peptide_confirm
+
 7. License
    =======
    LBEEP V1.0 is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation version 3.0 of the License.

dependency/module/brsaran/DDE.pm

@@ -43,7 +43,8 @@ sub DDE{		#Computes the Dipeptide Deviation from Mean
 		 }else{
 		     $i=0; 	
 		 }
-	     $pX[$j] = $i/$Length_Prt;	     	#Measure Calculation : px = nx/N
+	     if($Length_Prt <5){print "\nLength of peptide less than 6 is not acceptable ! Exiting !\n";exit;}
+	     $pX[$j] = $i/$Length_Prt;	     	#Measure Calculation : px = nx/N	
 	     $j++;
 	     $i=0;
     }
@@ -105,7 +106,7 @@ sub Epi_Predict_pep{ #Routine for making prediciton using model generated in WEK
 	my ($path) = $_[1];
 	my ($Model_sel) = $_[2];
 	my $mod_path;
-	if($Model_sel eq 'O'){ $mod_path = './model/ORIGINAL.model';}else{$mod_path = './model/BALANCED.model';}
+	if($Model_sel eq 'O'){ $mod_path = './model/ORIGINAL.model';}elsif($Model_sel eq 'C'){$mod_path = './model/CONFIRM.model';}else{$mod_path = './model/BALANCED.model';}
 	my $t;
 	$t = `java -cp $path./weka.jar weka.classifiers.meta.AdaBoostM1 -T $Arff_file -l $mod_path -p 0`;
 	return $t;

test_input_peptides

@@ -1,11 +1,18 @@
 >Test1
-WGAQLNAM
->PTest2
-LNAMKPDL
+NHNYPPLSLLTF
+>Test2
+SHDWRLMLSHLQ
 >Test3
-GDLVGPGC
+QHDRLLMLSYLV
 >Test4
-RLQGMAPAAGADLDK
+HHILPPKALLFG
 >Test5
-RAISSWKQRNRW
-
+SHTFPPSWLLVR
+>Test6
+YSVKPPLPYLPP
+>Test7
+NHNYPPLSLLTF
+>Test8
+SHKIHPFQTTPY
+>Test9
+HSPRYHSEPQFG