Supplementary Data- LBtope

DATA SET NAME Brief Description of Data
LBtope_Fixed We used truncation and extension technique used in previous studies to generate fixed length peptides (epitopes & non-epitopes) of 20 residues. Following procedure has been adopted to generate fixed length epitopes; i) all epitopes having less than 5 residues were removed, ii) epitopes having more than 20 residues were trimmed from both ends to generate epitope of 20 residues from middle iii) epitopes having less than 20 residues have been extended to 20 by adding equal number of residues at both end of epitope and iv) finally identical epitopes were removed. In summary, Lbtope_Fixed dataset contain 19803 unique positive patterns or B-cell epitopes and 28329 unique negative patterns or non B-cell epitopes, where each pattern has 20-residues. We also removed patterns common in both types of patterns. Our final Lbtope_fixed dataset contains 12063 B-cell epitopes and 20589 non-epitopes. More details

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LBtope_Fixed (Positive pattern)
LBtope_Fixed (Negative pattern)

Lbtope_Fixed_non_redundant Using Lbtope_Fixed dataset, we create an 80% non-redundant dataset using Cd-hit. The redundant dataset contain 7824 B-cell epitopes and 7853 non-epitopes.

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LBtope_Fixed_non_redundant (Positive pattern)
LBtope_Fixed_non_redundant (Negative pattern)

Lbtope_Variable We remove all epitopes or non epitopes having less than 5 residues or more than 50 residues. All epitopes common in B-cell epitopes and non B-cell epitopes were also removed. We found that majority of common epitopes are related to autoimmunity. Our final dataset Lbtope_Variable contain 14876 unique B-cell epitopes and 23321 unique non B-cell epitopes. More details

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LBtope_Variable (B cell epitopes)
LBtope_Variable (Non B cell epitopes)

Lbtope_Variable_non_redundant We again created an 80% non-redundant Lbtope_Variable dataset using Cd-hit. We obtain 8011 B-cell epitopes and 10868 non-epitopes.

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LBtope_Variable_non_redundant (B cell epitopes)
LBtope_Variable_non_redundant (Non B cell epitopes)

Lbtope_Confirm One of the challenges in creating dataset is its validity, though all epitopes we extracted from IEDB are experimentally tested. In order to improve quality of epitopes/non-epitopes, we only used epitopes/non-epitopes reported by at least two studies. The final dataset Lbtope_Confirm contain 1042 unique B-cell epitopes and 1795 unique non B-cell epitopes. More details

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LBtop_Confirm (B cell epitopes)
LBtop_Confirm (Non B cell epitopes)

OTHER DATA SETSDownload DataBrief Description of Data
ABCPredPositive pattern(20 mer)
Negative pattern(20 mer)
Positive pattern(16 mer)
Negative pattern(16 mer)
Dataset obtained from ABCPred Method.
Positive pattern(20 mer)
Negative pattern(20 mer)
Dataset obtained from Chen Method.
BCPredPositive pattern(20 mer)
Negative pattern(20 mer)
Dataset obtained from BCPred Method.