Help
ABOUT
This database is developed to provide the support to scientific community in searching and predicting the vaccine candidate regions of a highly deadly virus affecting bovine in india - Lumpy skin disease virus. In this database, users can find the vaccine candidate regions I.e B cell epitopes, T cell epitopes, MHC class 1 and class 2 peptides with respect to the Lumpy skin disease virus .
SEARCH
We have provided simple search option where user can search a particular peptide or genome id. User can click on the displayed peptides to go to a different page; which gives details of all the genome id’s that contain this particular peptide along with the individual results from all the different tables for that particular peptide.
BROWSE
This option allow user to select the desired database from the Dropdown menu which are as follow:
LBTOPE
The page is set to fetch data based on the percent probability of correct prediction for the given peptide where the fetched result is presented in the descending order. The default value of percentage is between 90 and 100 which can be manipulated by user to choose the range in which they want result.
CBTOPE
The page is set to fetch data based on the SVM score for the given peptide where the fetched result is presented in the descending order. The default value of SVM score is between 0 and 1 which can be manipulated by user to choose the range in which they want result.
MHC-1
The page is set to fetch data based on the NB (Number of Binders) for the given peptide where the fetched result is presented in the descending order. The default value of NB is between 164 and 190 which can be manipulated by user to choose the range in which they want result.
MHC-2
The page is set to fetch data based on the NB (Number of Binders) for the given peptide where the fetched result is presented in the descending order. The default value of NB is between 305 and 310 which can be manipulated by user to choose the range in which they want result.
CONSERVED EPITOPES
This option will fetch peptides that are conserved in all the 73 LSDV genomes for each B-cell & T-cell type. Similarly, the Soft-Conserve epitope option will show the epitopes present in >50-<100% of the LSDV genomes. Likewise, the unique option will show epitopes present in less than 50% of the genomes.
GENOME
This option provide the in-depth summary of each LSDV genome like CpG island, codon frequency, virulence genes, capsid protein, Genes containing signal sequences and transmembrane helix etc.
Structure
This option is use to visualize the protein strcutre of LSDV gene predicted by I-tasser software.
EPITOPE MAPPING
Additionaly, we have provided the option to view the peptide epitope mapped on reference protein along with the mutational site if present. The default protein is set in wireframe view with ribbon color for peptide epitope and ball-stick model for mutation position. This option help the user to know whether the peptide epitope is on protein surface or burried as well as the mutation if present.
ADVANCED SEARCH
This option allows users to filter the search results on various parameters along with selecting the required database. Users can search both with or without the Peptide.
MHC-1
In MHC-1, users can select the various alleles form which they want result, also they can choose the El Score for those selected alleles. The EL Score for Weak Binders is Between 0.500 and 2.000 and for Strong Binders it is below 0.500 . NB at the end of the table Denotes Number Of Binders for all the alleles(Total number of alleles are 172.)
MHC-2
In MHC-2, users can select the various alleles form which they want result, also they can choose the El Score for those selected alleles. The EL Score for Weak Binders is Between 1.00 and 5.000 and for Strong Binders it is below 1.00 . NB at the end of the table Denotes Number Of Binders for all the alleles(Total number of alleles are 309.)
CBTOPE
This option help users to select the prediction score (SVM Score), greater the SVM Score, Better the peptide.
LBTOPE
In this option, user can select the parameter from the dropdown menue and can set the score between which they want result.
TOOLs
BLAST
The standalone BLAST is integrated in the database to help the user for identifying similar sequences from LSDV genome. User can select the database type (DNA/Protein), e-value, coverage and maximum hits for single query to limit the search.
DOT PLOT
This tool basically take two genomic DNA sequences to compare the similarity between them and plot the graph in the two dimentional dots.
G-BLOCK
This tool take a muliple sequence alignment of either the DNA or protein as input. Based on the user selected option like minimum length of block and no. of non -conserved residue present continously, it can find the conserved region in the genome.
DESIGN PRIMER
This option is useful to the users interested in designing of primer for a user specific sequence. User just need to put the sequence in fasta format and can select the option. After click on Design Primer button, the database run primer3 software & output five best primer for the given query sequence.
DESIGN gRNA
This tool is used for designing the gRNA by selecting the gene present in LSDV genome. Here, the user can specify the gRNA length, PAM sequence, coverage and identity option. This is an in-house script that will showed the gRNA location in gene, its sequence, GC content, no. of on and off targets.