Lasergene

Lasergene performs comprehensive DNA and protein sequence analysis to enable genomic, proteomic, and immunological investigations including sequence assembly, single nucleotide polymorphism (SNP) detection, automated virtual cloning, primer design, and B cell epitope prediction.

Key Features:

• DNA and protein sequence analysis: Performs comprehensive analyses of DNA and amino acid sequences.
• Sequence assembly: Provides functionality for sequence assembly.
• Single nucleotide polymorphism (SNP) detection: Detects single nucleotide polymorphisms (SNPs) within sequence data.
• Automated virtual cloning: Supports automated virtual cloning operations.
• Primer design: Designs primers for downstream experimental workflows.
• DNAStar Protean B cell epitope prediction: Includes the DNAStar Protean system for prediction and selection of potential B cell epitopes.
• Analysis of viral structural proteins: Analyzes complete amino acid sequences of viral structural proteins for epitope and sequence-based investigations.

Scientific Applications:

• B cell epitope identification: Identification of B cell epitopes on viral proteins, exemplified by analysis of foot-and-mouth disease virus (FMDV) serotype Asia1 structural proteins.
• Epitope candidate generation: Bioinformatics analysis produced seventeen peptide candidates for B cell epitopes in the FMDV Asia1 study.
• Validated epitope sequences: Six peptides validated by sera from rabbits immunized with the FMDV type Asia1 P1 polyprotein were epi1-1 (VP1: TTTTGESADPVT), epi1-2 (VP1: NYGGETQTARRLH), epi1-6 (VP1: TTQDRRKQEIIAPEKQTL), epi2-2 (VP2: EDAVSGPNTSG), epi3-1 (VP3: YGKVSNPPRTSFPG), and epi4-2 (VP4: YQNSMDTQLGDN).
• Support for experimental validation: Facilitates selection of peptides for cloning into vectors such as pGEX-6P-1, expression as glutathione S-transferase (GST) fusion peptides, and antigenicity testing by Western blot and ELISA.
• Vaccine design assistance: Aids vaccine design efforts by mapping B cell epitopes on viral proteins.

Methodology:

Analysis of complete amino acid sequences of FMDV serotype Asia1 structural proteins and prediction and selection of potential B cell epitopes using the DNAStar Protean system.