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Pinky Sheetal V M.Tech Bioinformatics


Experiment 2: Genome Rearrangement
Aim: To analyze the genome rearrangement between two chromosomal genomes using SPRING
Tool
Introduction:
The genome of an organism consists of a long string of DNA, cut into a small number of
segments called chromosomes. Genes are stretches of the DNA sequence that are responsible for
encoding proteins. Each gene has an orientation, either forward or backward, depending in which
direction it is supposed to be read. A chromosome can thus be abstracted as an ordered set of
oriented genes. Higher organisms' chromosomes are linear (their DNA sequence has a beginning
and an end), but for lower organisms like bacteria, the chromosome is circular (their DNA
sequence has no beginning or end). The most common and most studied mutations operating on
DNA sequences are local: they affect only a very small stretch on DNA sequence. These
mutations include nucleotide substitutions (where one nucleotide is substituted for another), as
well as nucleotide insertions and deletions. Most phylogenetic studies have been based on these
types of mutations. Genome rearrangement is a different class of mutation affecting very large
stretches of DNA sequence. A genome rearrangement occurs when a chromosome breaks at two
or more locations (called the breakpoints), and the pieces are reassembled, but in the wrong"
order. This results in a DNA sequence that has essentially the same features as the original
sequence, except that the order of these features has been modified. If the chromosome breaks
occur in non-functional sequence, the rearrangement is unlikely to have any deleterious effects.
On the other hand, a rearrangement whose breakpoints fall in functional sequence (e.g. genes)
will almost certainly make the gene dysfunctional, rendering the organism unlikely to survive.
Consequently, almost all genome rearrangements that become fixed in future generations involve
inter-genetic breakpoints.

Tools:
SPRING-
SPRING (http://algorithm.cs.nthu.edu.tw/tools/SPRING/) is a tool for the analysis of genome
rearrangement between two chromosomal genomes using reversals and/or block-interchanges.
SPRING takes two or more chromosomes as its input and then computes a minimum series of
reversals and/or block interchanges between any two input chromosomes for transforming one
chromosome into another. The input of SPRING can be either bacterial-size sequences or
gene/landmark orders. If the input is a set of chromosomal sequences then the SPRING will
automatically search for identical landmarks, which are homologous/conserved regions shared
by all input sequences. In particular, SPRING also computes the breakpoint distance between
any pair of two chromosomes, which can be used to compare with the rearrangement distance to
confirm whether they are correlated or not. In addition, SPRING shows phylogenetic trees that
are reconstructed based on the rearrangement and breakpoint distance matrixes. LCBs (Locally
Collinear Blocks) are identical landmarks, which are homologous/conserved regions shared by
all input sequences. Basically, an LCB is a collinear set of multi-MUMs (which are exactly
matching subsequences shared by all chromosomes considered that occur only once in each
chromosome and that are bounded on either side by mismatched nucleotides). In practice, it may
correspond to a homologous region of sequence shared by all genomes and does not contain any
genome rearrangements.
Pinky Sheetal V M.Tech Bioinformatics


Protocol:
   1. Retrieve query from NCBI-
      Sequence 1:
      >gi|363806631|emb|FQ976726.3| Susscrofachromosome Y clone WTSI_1061-69M2
          Sequence 2:
          >gi|363806635|emb|FQ976728.4| Susscrofa chromosome Y clone WTSI_1061-70O20
   2. Input the sequence inSPRING.
   3. View Results.
Result:




Interpretation:
S1 LCB:
LCB Number, Left and Right End Coordinates of LCB (LCB's Length, LCB's Weight)
1. 28262 : 28855 (594, 115)
2. 28973 : 33435 (4463, 1022)
The total LCBs cover 13.92% of the genome.
Pinky Sheetal V M.Tech Bioinformatics


S2 LCB:
LCB Number, Left and Right End Coordinates of LCB (LCB's Length, LCB's Weight)
1. -26444 : -25669 (776, 115)
2. 12656 : 22329 (9674, 1022)
The total LCBs cover 29.19% of the genome.
Since both coordinates are negative, they are inverted region on the opposite strand of the given
sequence.

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Genome rearrangement

  • 1. Pinky Sheetal V M.Tech Bioinformatics Experiment 2: Genome Rearrangement Aim: To analyze the genome rearrangement between two chromosomal genomes using SPRING Tool Introduction: The genome of an organism consists of a long string of DNA, cut into a small number of segments called chromosomes. Genes are stretches of the DNA sequence that are responsible for encoding proteins. Each gene has an orientation, either forward or backward, depending in which direction it is supposed to be read. A chromosome can thus be abstracted as an ordered set of oriented genes. Higher organisms' chromosomes are linear (their DNA sequence has a beginning and an end), but for lower organisms like bacteria, the chromosome is circular (their DNA sequence has no beginning or end). The most common and most studied mutations operating on DNA sequences are local: they affect only a very small stretch on DNA sequence. These mutations include nucleotide substitutions (where one nucleotide is substituted for another), as well as nucleotide insertions and deletions. Most phylogenetic studies have been based on these types of mutations. Genome rearrangement is a different class of mutation affecting very large stretches of DNA sequence. A genome rearrangement occurs when a chromosome breaks at two or more locations (called the breakpoints), and the pieces are reassembled, but in the wrong" order. This results in a DNA sequence that has essentially the same features as the original sequence, except that the order of these features has been modified. If the chromosome breaks occur in non-functional sequence, the rearrangement is unlikely to have any deleterious effects. On the other hand, a rearrangement whose breakpoints fall in functional sequence (e.g. genes) will almost certainly make the gene dysfunctional, rendering the organism unlikely to survive. Consequently, almost all genome rearrangements that become fixed in future generations involve inter-genetic breakpoints. Tools: SPRING- SPRING (http://algorithm.cs.nthu.edu.tw/tools/SPRING/) is a tool for the analysis of genome rearrangement between two chromosomal genomes using reversals and/or block-interchanges. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block interchanges between any two input chromosomes for transforming one chromosome into another. The input of SPRING can be either bacterial-size sequences or gene/landmark orders. If the input is a set of chromosomal sequences then the SPRING will automatically search for identical landmarks, which are homologous/conserved regions shared by all input sequences. In particular, SPRING also computes the breakpoint distance between any pair of two chromosomes, which can be used to compare with the rearrangement distance to confirm whether they are correlated or not. In addition, SPRING shows phylogenetic trees that are reconstructed based on the rearrangement and breakpoint distance matrixes. LCBs (Locally Collinear Blocks) are identical landmarks, which are homologous/conserved regions shared by all input sequences. Basically, an LCB is a collinear set of multi-MUMs (which are exactly matching subsequences shared by all chromosomes considered that occur only once in each chromosome and that are bounded on either side by mismatched nucleotides). In practice, it may correspond to a homologous region of sequence shared by all genomes and does not contain any genome rearrangements.
  • 2. Pinky Sheetal V M.Tech Bioinformatics Protocol: 1. Retrieve query from NCBI- Sequence 1: >gi|363806631|emb|FQ976726.3| Susscrofachromosome Y clone WTSI_1061-69M2 Sequence 2: >gi|363806635|emb|FQ976728.4| Susscrofa chromosome Y clone WTSI_1061-70O20 2. Input the sequence inSPRING. 3. View Results. Result: Interpretation: S1 LCB: LCB Number, Left and Right End Coordinates of LCB (LCB's Length, LCB's Weight) 1. 28262 : 28855 (594, 115) 2. 28973 : 33435 (4463, 1022) The total LCBs cover 13.92% of the genome.
  • 3. Pinky Sheetal V M.Tech Bioinformatics S2 LCB: LCB Number, Left and Right End Coordinates of LCB (LCB's Length, LCB's Weight) 1. -26444 : -25669 (776, 115) 2. 12656 : 22329 (9674, 1022) The total LCBs cover 29.19% of the genome. Since both coordinates are negative, they are inverted region on the opposite strand of the given sequence.