synetny and the world of genomics

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..