WEB DOCUMENTATION
- Sequence Submission:
The sequence submission form can be found at http://vac.kamalrawal.in/vaxidl. One or more protein sequences in FASTA format or one UniProt ID can be pasted into the text box, or the "Browse..." option can be used to analyze a file of one or more sequences stored in the user's computer. Also, choose the appropriate input format based on your input. Optionally, you can provide your email address to receive a notification of result link.
The sequence submission form can be found at http://vac.kamalrawal.in/vaxidl. One or more protein sequences in FASTA format or one UniProt ID can be pasted into the text box, or the "Browse..." option can be used to analyze a file of one or more sequences stored in the user's computer. Also, choose the appropriate input format based on your input. Optionally, you can provide your email address to receive a notification of result link.
Please note that the following restrictions are enforced:
i. Minimum 30 residues per sequence are required
ii. Maximum 4000 residues per sequence are allowed
iii. Maximum 200000 total residues in the input are allowed
iv. Only protein sequence is allowed
v. Only FASTA format is allowed
Please note that the following restrictions are enforced:
i. Minimum 30 residues per sequence are required
ii. Maximum 4000 residues per sequence are allowed
iii. Maximum 200000 total residues in the input are allowed
iv. Only protein sequence is allowed
v. Only FASTA format is allowed
2. Choose ensemble model approach:
2. Choose ensemble model approach:
There are 2 different models with different ensemble approaches:
i. Consensus-based approach
ii. Average-based approach
There are 2 different models with different ensemble approaches:
i. Consensus-based approach
ii. Average-based approach
In the consensus-based approach, 5 individual models are used and the consensus of all the 5 individual models is considered to be the final result. Since the model considers the final classification of individual models i.e., 0 or 1 (non-vaccine candidate or vaccine candidate), the final probabilities get lost, and therefore percentage probability is not generated for this approach.
In the consensus-based approach, 5 individual models are used and the consensus of all the 5 individual models is considered to be the final result. Since the model considers the final classification of individual models i.e., 0 or 1 (non-vaccine candidate or vaccine candidate), the final probabilities get lost, and therefore percentage probability is not generated for this approach.
In the average-based approach, the average output of all the 5 individual models is taken as the final result. Since the model averages the raw output of each model, the final probabilities are also the average of each probability and therefore percentage probability is generated for this approach.
In the average-based approach, the average output of all the 5 individual models is taken as the final result. Since the model averages the raw output of each model, the final probabilities are also the average of each probability and therefore percentage probability is generated for this approach.
3. Receiving results:
3. Receiving results:
There are two ways to receive results from Vaxi-DL i.e. via email (contains result link) or wait for screen display (wait till analysis is completed and then automatically the user is redirected to the result link or you can bookmark this page to check later).
There are two ways to receive results from Vaxi-DL i.e. via email (contains result link) or wait for screen display (wait till analysis is completed and then automatically the user is redirected to the result link or you can bookmark this page to check later).
After a successful analysis of the input, the result link will be provided to the user via email if provided. In case, the server is unable to parse the user's input or the server encounters an exception during analysis, an explanation for the same will be sent to the user via email or you can check the earlier bookmarked page for an explanation.
After a successful analysis of the input, the result link will be provided to the user via email if provided. In case, the server is unable to parse the user's input or the server encounters an exception during analysis, an explanation for the same will be sent to the user via email or you can check the earlier bookmarked page for an explanation.
If email is provided then you will receive an notification,
If email is provided then you will receive an notification,
4. Acceptable Formats:
4. Acceptable Formats:
Vaxi-DL requires PROTEIN sequences to be submitted in FASTA format only.
Vaxi-DL requires PROTEIN sequences to be submitted in FASTA format only.
A sequence within a FASTA sequence file consists of three parts:
i. A title line, that must begin with the '>' symbol and may be followed by any type of text
ii. A newline character at the end of the title line
iii. The sequence itself, which continues until the end of the file or the next '>' is reached
A sequence within a FASTA sequence file consists of three parts:
i. A title line, that must begin with the '>' symbol and may be followed by any type of text
ii. A newline character at the end of the title line
iii. The sequence itself, which continues until the end of the file or the next '>' is reached