Pinky SheetalM.Tech BioinformaticsExperiment 1: Genome ComparisonAim: To analyze the genome by genome comparison using different genome analysis toolsIntroduction:A complete genome sequence of an organism can be considered to be the ultimate genetic map,in the sense that the heritable characteristics are encoded within the DNA and that the order of allthe nucleotides along each chromosome is known. However, knowledge of the DNA sequencedoes not tell us directly how this genetic information leads to the observable traits and behaviors(phenotypes) that we want to understand. The information got by finding all the functional partsof genome sequences can be used to improve the health of individuals and society. Commonfeatures of two organisms will often be encoded within the DNA that is conserved between thespecies. More precisely, the DNA sequences encoding the proteins and RNAs responsible forfunctions that were conserved from the last common ancestor should be preserved incontemporary genome sequences. Likewise, the DNA sequences controlling the expression ofgenes that are regulated similarly in two related species should also be conserved. Conversely,sequences that encode (or control the expression of) proteins and RNAs responsible fordifferences between species will themselves be divergent.Tools: 1. Genome VISTA http://pipeline.lbl.gov/cgi-bin/gateway2 Genome VISTA is an automatic server that allows the user to find candidate orthologous regions for a draft or finished DNA sequence from any species on a base genome, and provides detailed comparative analysis. Genome VISTA uses a computational strategy where query sequence contigs are anchored on the base genome by local alignment matches (Kent, 2002) and then globally aligned to candidate regions by AVID program. A sequence up to 300 kilobases long can be submitted by pasting it into a window in plain Fasta format: • By uploading Fasta file from your computer, • Or by providing GenBank accession number to the server 2. GenomeBlast http://bioinfo-srv1.awh.unomaha.edu/genomeblast/ GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each genome; (2) homologous gene candidates among compared genomes; (3) 2D plots of homologous gene candidates along the all pairwise genome comparisons; and (4) a table of gene presence/absence information and a genome phylogeny.Protocol: 1. Retrieve the genome of an organism from NCBI- Genome (eg: Mycobacterium gi-903) 2. Access Genome VISTA and enter the accession number.
Pinky SheetalM.Tech BioinformaticsChromosome 1 is similar to 2 sets of chromosomes:chr1:201,401,002-201,401,662 (660bp)chr1:201,364,507-201,364,935 (428bp)Interpretation:Sequence 1 is similar to Mouse chromosome 1, Rat chromosome 13, Chicken chromosome 26,Dog chromosome 7, Rhesus chromosome 1 and Horse chromosome 30.