2015.11.25修改《生物信息学》实验操作指导.doc

《生物信息学》实验操作指导 杭州师范大学生命与环境科学学院 向太和 PAGE PAGE 29 Experiments in Bioinformatics Content Experiment 1 Analysis of DNA sequence………….….……2-4 Experiment 2 Analysis of protein sequence………….….5-8 Experiment 3 Multiple sequence alignments…………9-11 Experiment 4 Analysis of gene function…………..……..12-13 Experiment 5 Literature retrieval using PubMed……14-19 Experiment 6 Design primers for PCR and draw a plasmid map…………………………….20-21 Appendix Useful website address………..………...…22-30 Experiment 1 Analysis of DNA sequence THE PURPOSE 1. Molecular databases: you will learn how to use and understand molecular databases that store the wealth of information that is so useful to the molecular biologist, such as finding and retrieving sequence in public databases, how to read the coding of database entries, etc. 2. Similarity searching: perform your own similarity searches of provided “unknown” sequences on the nucleotide databases with Blast, the most popular sequence alignment search tool. You have been given an unknown sequence to identify, but no clues as to what it is. The provider wants an unbiased opinion. LIST OF MATERIALS AND TOOLS cab or SOD gene sequences; GenBank accession number: AY580883.1 Unknown DNA sequences: X1 1 gacatactct actactacta gccagtaagc tagctaacta actacgtggc tatggccccc 61 accgtgatgg cctcctcggc cacctccgtg gctccattcc aagggctcaa gtccaccgcc 121 gggctccccg tcagccgccg ctccaccaac tcgggcttcg gcaacgtcag caatggcgga 181 aggatcaagt gcatgcaggt gtggccaatt gagggcatca agaagttcga gaccctatcg 241 tacctgccac cactcaccgt ggaggatctt ttgaagcaga tcgagtacct gcttcgatcc 301 aagtgggtgc cttgcctcga gttcagcaag gttggattcg tctaccgtga gaaccacagg 361 tctcccgggt actacgatgg caggtattgg accatgtgga agctgcccat gttcggctgc 421 accgatgcca cccaggtgct caaggagctc gaggaggcca agaaggccta ccccgatgcc 481 tttgtccgta tcatcggctt cgacaacgtc aggcaggtgc agttgattag cttcatcgcc 541 tacaagcccc caggttgcga ggagtctgg