JAWAHARLAL NEHRU TECHNOLOGICAL UNIVERSITY HYDERABAD B.Pharmacy III BIOINFORMATICS Previous Question Paper (November/December-2020 - R17)

(i) The World Wide Web (WWW) is an information system where documents and other web resources are identified by Uniform Resource Locators (URLs), interlinked by hypertext links, and accessible via the Internet. It serves as the primary interface for users to navigate and retrieve data across global networks.

(ii) HTTP (Hypertext Transfer Protocol) is the foundational application-layer protocol used for transmitting hypermedia documents, such as HTML, on the web. It functions as a request-response protocol in the client-server computing model, where a web browser acts as the client and a server hosting the website acts as the server.

Protein sequence annotation from mass spectral data follows a systematic computational pipeline:

1. Data Pre-processing: Raw mass spectra are cleaned to remove noise, perform baseline correction, and de-isotope the peaks to identify monoisotopic masses.
2. Peak List Generation: Conversion of raw spectra into a list of mass-to-charge (m/z) ratios and their corresponding intensities.
3. Database Searching: The processed spectral data is searched against known protein sequence databases (e.g., UniProt) using algorithms like Mascot or SEQUEST to match experimental spectra with theoretical spectra generated from protein sequences.
4. De Novo Sequencing: If the protein is novel or not in the database, de novo sequencing is performed to determine the amino acid sequence directly from the fragmentation pattern of the peptides.
5. Annotation and Validation: Identified sequences are mapped to functional protein databases to assign biological functions, domains, and post-translational modifications, followed by statistical validation using false discovery rates (FDR).