Bioinformatics Exercise 4

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BIOL 4200 Bioinformatics
DNA, RNA, and protein structure exercises; MEGA5

This summary exercise focuses on the survey of the databases of RNA and protein structures with the goal of searching these databases to identify DNA or protein sequences that might be appropriate for your class project. This exercise will also start the phylogenetic analysis of DNA and protein sequences using MEGA5

Name: Sohaib Iqbal

1. Please click through these websites of RNA and protein structures. Please describe briefly what these websites are, in other words, what biological research activities you can conduct using these websites. Please rephrase your words, do not copy and paste, for any information you obtain from any other sources.

Vienna RNA package: RNA Secondary Structure Prediction and Comparison http://www.tbi.univie.ac.at/RNA/ * This website shows research group bioinformatics and computational biology. This website represents the Institute of Theoretical Chemistry, which is a part of University of Vienna. They use and develop algorithms to detect RNA genes, folding dynamics of melecules, RNA design and chemical reaction networks.

Vienna RNA webservers: http://rna.tbi.univie.ac.at/

* This page shows programs and web services that can be used to show and discuss RNA secondary structures. They also consist of folding kinetics, sequence design, and genome wide screening.

tRNAscan-SE Search Server: http://lowelab.ucsc.edu/tRNAscan-SE/

* This website is useful for running tRNA scan-SE servers, analyzing tRNAs in a published genome and interpreting outputs. You can also run tRNA scan-SE locally, but you need a UNIX source code. Additionally, this website is great for tRNA genes in genomic sequence.

RNA families: http://rfam.sanger.ac.uk/

* This website allows users to access RFAM database, which is a collection of RNA families. A…...

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