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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.
Pinky SheetalM.Tech Bioinformatics


   3. Submit
Results:
Pinky SheetalM.Tech Bioinformatics
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.

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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.
  • 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.