Genome comparision

1. Pinky SheetalM.Tech Bioinformatics
Experiment 1: Genome Comparison
Aim: To analyze the genome by genome comparison using different genome analysis tools
Introduction:
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 all
the nucleotides along each chromosome is known. However, knowledge of the DNA sequence
does 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 parts
of genome sequences can be used to improve the health of individuals and society. Common
features of two organisms will often be encoded within the DNA that is conserved between the
species. More precisely, the DNA sequences encoding the proteins and RNAs responsible for
functions that were conserved from the last common ancestor should be preserved in
contemporary genome sequences. Likewise, the DNA sequences controlling the expression of
genes 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 for
differences 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.

2. Pinky SheetalM.Tech Bioinformatics
3. Submit
Results:

3. Pinky SheetalM.Tech Bioinformatics

4. Pinky SheetalM.Tech Bioinformatics
Chromosome 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.