The Comparative genomics is one of my interest where in India many
people knows bioinformatics as a designing drug, simulation, and protein
folding, predicting 3D structures.but i gotta a right place to do ... i will
share what i know the little which i learnt...
Comparative genomics:
The comparative genomics is the one of the bioinformatics approach
here we can compare the unknown genomes with known genomes by the genome size,
no of genes and chromosome. by comparing the two genome we can identify the
core set of genes between two organisms, we can identify the genes which is
involved in mutation or ability to cause diseases also.. the comparative
genomics it reveals the evolutionary relationships of an organisms
Synteny? The two or more genes which are located on
the same chromosome and the linkage between them ie genes. most likely
the chromosome is based on collinearity data that two or more
chromosomes or segments are derived from a common ancestor, we can say that
synteny is likely used to identify the homologous genes to the ancestral
chromosomal position.for example in human we all know we have 23 pairs of
chromosome and the human chromosome 17 corresponds to the entire portion of
mouse chomosome 11.
some terms related to synteny:
Single gene transposition:
it refers to the insertion of one
gene into a new location
Fractionation:
here by which the duplicated gene,
chromosomal segment , genome organization tends to return to its preduplication
gene content
Subfunctionalization:
selectively
neutral tendency of a duplicated cis-acting unit of function to lose
dispensable sequences on one but not both, duplicates, such that the
ancestral function is spread over both duplicates
COGE is one of the
online database used for analysing the synteny
the identification
of syntenic regions can be done by
1. finding the
putative regions or homologous genes between the two genomes.
2. identifying
the co-linear set of genes or the regions of sequence similarity
synmap methods:
1. extracts the
sequence for comparison builds the fasta files.
2.it creates the
database and compare using the BLAST algorithm
3.It contains the
default e value cutoff of 0.001
4. it identify
tandem gene duplicates by blast2raw.
5. it filters the
repetitive matches
6.identify the
syntenic pairs by finding co-linear putatative homologous sequences.
7. it calculates
the synonymous and non synonymous mutation rates for syntenic gene pairs.
8.it generates the
dotplot for putative homologous matches.
9. the colored
dotplots based on the synonymous and nonsynonymous mutations.
Analysis
options:
1. breaks the
sequences into multiple pieces and searches
2
filter repetitive matches:
it adjusts the
evalues of the blast hits to lower the significance of sequence that occurs in
multiple times in genome.
3. DAG chainer
options:
identify synntenic
regios between genomes and gene spaces in genomes.
4. average distance
between syntenic regions.
5.maximum distance
between two matches.
6. minium range of
aligned pairs
7. syntenic depth:
it gives the best syntenic regios that covers each genome.
the syntenic dotplot which is constructed between Ecoli genomes.. iam just giving this an example so that everybody can have an idea of dotplot and how it looks..
