Complete viral protein sequences were downloaded from two publicly available databases, NCBI (Brister et al. 2015 (link)) and Viper (Pickett et al. 2012 (link)), respectively. NS1 sequences were retrieved and filtered to obtain a set of complete and unique sequences. SE (Litwin and Jores 1992 ) was calculated to understand the diversity at each amino acid position. This study's reference strains were as follows: DENV1: Accession number KM204119.1, DENV2: Accession number U87411.1, DENV3: Accession number KU050695.1 and DENV4: Accession number KR011349.2 were retrieved from NCBI. Subsequently, an intense literature survey was done to identify structurally and functionally critical residues. A Python script was written to analyze the temporal and geographical distribution of NS1.
Protocol detail
Comprehensive Analysis of DENV NS1 Diversity
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Corresponding Organization : Indian Institute of Science Bangalore
Other organizations : Indian Institute of Technology Goa
Top 5 similar protocols
Variable analysis
independent variables
- Complete viral protein sequences downloaded from NCBI and Viper databases
- Retrieval and filtering of NS1 sequences to obtain a set of complete and unique sequences
- Sequence Entropy (SE) calculated to understand the diversity at each amino acid position
- Temporal and geographical distribution of NS1 analyzed using a Python script
- Reference strains for DENV1, DENV2, DENV3, and DENV4 retrieved from NCBI
- Structurally and functionally critical residues identified through literature survey
- No positive or negative controls explicitly mentioned
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
Sign up for free or login to display all annotations
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!