Questions 1. Search Pubmed using the following keywords How do I search Pubmed?

What is the role of smoking in Lung neoplasm? Use the operators (AND, OR, NOT) for the keyword search. 2. How do I search by author? [Ramachandran GN] an GN" Search Pubmed using the author name as "Ramachandrand list number of publications. And also find out how many citations for the article "Theory of the non-planar peptide unit" for the same author. 3. Download the original article "DNA double helix structure" published by Watson and crick? Write few lines about the article and list out the publication date, publisher and their affilations 4. Write few words (250 words) about a recent interesting article you read in open access. 5. Make list of these databases a) List three nucleotide sequence databases b) List out three protein sequence databases c) Any five eukaryotic gene expression databases [Look into this category Microarray Data and other Gene Expression Databases] d) Any three proteomics related databases e) Any three metabolic and signaling pathway databases f) Any five organelle databases g) List three protein structure databases h) List out three small molecule structure databases Make the references [pubmed id or pubmed central id] as bibliography in your ncbi web account.

6. Make the list for the following tools a) List two local alignment tools b) List two Global alignment tools c) List two Phylogenetic analysis tools d) List two protein structure visualization tools e) Make the references [pubmed id or pubmed central id] as bibliography in your ncbi web account.

7. How do you convert plain sequence into FASTA format [protein name: DmpR, gi: 483552, organism: Pseudomonas sp. CF600] MPIKYKPEIQHSDFKDLTNLIHFQSMEGKIWLGEQRMLLLQFSAMASFRREMVNTLGIERAKGLFLRHGY QSGLKDAELARKLRPNASEVGMFLAGPQMHSLKGLVKVRPTELDIDKEYGRFYAEMEWIDSFEVEICQTD LGQMQDPVCWTLLGYACAYSSAFMGREIIFKEVSCRGCGGDKCRVIGKPAEEWDDVASFKQYFKNDPIIE ELYELQSQLLSLRTNLDKQEGQYYGIGQTPAYQTVRNMMDKAAQGKVSVLLLGETGVGKEVIARSVHLRS KRAAEPFVAVNCAAIPPDLIESELFGVEKGAFTGATQSRMGRFERADKGTIFLDEVIELSPRAQASLLRV LQEGELERVGDNRTRKIDVRVIAATHEDLAEAVKAGRFRADLYYRLNVFPVAIPALRERREDIPLLVEHF LQRFHQEYGKRTLGLSDKALEACLHYSWPGNIRELENVIERGIILTDPNESISVQALFLRAPEEPQTASE RVSLDGVLIQPGNGQGSWISQLLSSGLSLDEIEESLMREAMQQANQNVSGAARLLGLSRPALAYRLKKIG IEG b) Write the name, position and patterns available in the given protein sequence using Prosite Pattern database. 8. Draw a dotplot for these two sequences [Use any available too] DILVDEQ IVQDEQ 9. Retrieval of Nucleic acid sequence a. Download the sequence of GI number (GenInfo identifier) 168825 b. Mention the gene name along with the scientific name of the organism which it belongs to.

10. Retrieval of Protein sequence a. Download the sequence of GI number (GenInfo identifier) 11066970 b. Mention the gene name along with the scientific name of the organism which it belongs to. 11. Find out DNA molecular weight for the given sequence using Sequence Manipulation Suite. GGACGGATCC 12. Download the protein sequence for the given gi number and perform multiple sequence alignment using ClustalW [529353, 58324, 168826] and interpret the results. 13. Perform protein blast against PDB for the protein sequence 33440070 (GI number) a. Mention the nearly identical protein structure you got b. List out the Query coverage of Identities, Positives & Gaps of the template c. Name the domains present in the given sequence 14. Downloading pdb structure for the given PDBID 3NJV a. By which technique the structure was determined. b. How many related entries present c. Name the source organism of the protein.

15. Visualization of protein structure (PDBID

1lyz) using Chimera

a) Draw a figure labeling its active site residues.

[http://www.pdb.org/pdb/101/motm.do?momID=142] 16. Perform pdbsum analysis for the given PDBID - 1C9C a. What are the ligands [hetro atoms] present in the protein (other than water) b. Whether disulphide bridges are present or not c. How many helices and strands are there 17. Pubchem small molecule search pubchem compound id - 32893 a. Write the molecular formula, how many hydrogen bond donors and acceptors are present,Download the 3d structure in sdf format and take picture using Chimera 18. Write few applications of bioinformatics using already published literature [Laccase wide spread in bacteria, Reconstructing the Origin of Andaman Islanders, Genomic databases yield novel bioplastic producers]