BTE-401 BIOINFORMATICS Assignment-1 BTE-401 BIOINFORMATICS Assignment-1 Marks: 15 1

BTE-401 BIOINFORMATICS Assignment-1
BTE-401 BIOINFORMATICS Assignment-1 Marks: 15 1. Choose Two diseases of your liking. These diseases should have following features: 2 a. Disease 1: Adequately researched with available publications b. Disease 2: Complex disease involving a few genes Provide ample justification for your choice. Tips: Try to avoid very common diseases to ensure unique results. Check beforehand if enough information is present about a disease before you choose it for assignment. 2. For Disease 1, go to PubMed and: a. Find the list of 8 most relevant publications; retrieve the Summary information for 5 of these publications. 1.25 b. Find the list of 6 most recent publications; retrieve the PMIDs for 4 of these publications. 1.5 c. Find the list of 10 most recent publications that provide Full Text; retrieve the Abstracts for 7 of these publications. 1.75 d. Find 7 publications with Full Articles available at PMC; access and explore 3 of these publications. 1 3. For Disease 2: a. Go to NCBI and find out the list of top 12 Human genes most related to the disease. Name this list as List A. 1 i. Retrieve the information about the genes in Tabular format. ii. Show how to display the retrieved Tabular file. b. Go to the Gene entry for the 6 th Gene in List A. 2 i. Identify the Genomic position of the Gene. ii. Browse the Genomic Location of the Gene and show related components. iii. Go to the mRNA and Protein entries of the most common isoform of the Gene and explore. iv. Show the RefSeq sequence of the Gene. c. Search for the SNPs related to the 5 th Gene in List A. 1.25 i. Find out if there are any pathogenic SNPs identified for the gene. ii. Describe the contents of the 4 th SNP entry from the search result. d. Search for the disease in OMIM. 1.25 i. Show what information is available about the disease under its entry. Note: Gene entries are not Disease entries. ii. Summarize the genetic information related to the disease. e. From List A, retrieve the names of 3 rd, 9th, 11th, and 12th Genes. 2 i. Go to Ensembl and use archived Ensembl 105. ii. Enter Biomart. iii. Retrieve features of these genes in tabular format (at least 6 features). Show which features were selected. iv. Retrieve structural information about the genes in tabular format (at least 5 structural features not retrieved in iii). Show which features were selected.