Difference between revisions of "GEvo"
From CoGepedia
(→Introduction) |
(→Introduction) |
||
| Line 19: | Line 19: | ||
=== Alignment Algorithms === | === Alignment Algorithms === | ||
Current GEvo can use: | Current GEvo can use: | ||
| − | *BlastZ: DNA-DNA Local Alignment Algorithm. Good for finding large regions of conserved sequence. | + | *[http://www.bx.psu.edu/miller_lab/ BlastZ:] DNA-DNA Local Alignment Algorithm. Good for finding large regions of conserved sequence. |
| − | *BlastN: DNA-DNA Local Alignment Algorithm. Good for finding small regions of conserved sequence. | + | *[http://blast.ncbi.nlm.nih.gov/Blast.cgi BlastN:] DNA-DNA Local Alignment Algorithm. Good for finding small regions of conserved sequence. |
| − | *TBlastX: Translated DNA-Translated DNA Local Alignment Algorithm. Good for finding small regions of divergent, but evolutionarily conserved, genomic sequence where protein translated sequence is more conserved than DNA sequence. | + | *[http://blast.ncbi.nlm.nih.gov/Blast.cgi TBlastX:] Translated DNA-Translated DNA Local Alignment Algorithm. Good for finding small regions of divergent, but evolutionarily conserved, genomic sequence where protein translated sequence is more conserved than DNA sequence. |
*Chaos: DNA-DNA Local Alignment Algorithm. Good for finding small regions of conserved sequence. Uses fuzzy matches so it can seed its alignment on small sequences than BlastN. However, it is slower than BlastN. | *Chaos: DNA-DNA Local Alignment Algorithm. Good for finding small regions of conserved sequence. Uses fuzzy matches so it can seed its alignment on small sequences than BlastN. However, it is slower than BlastN. | ||
*[http://bibiserv.techfak.uni-bielefeld.de/dialign/ DiAlign:] DNA-DNA Global Alignment Algorithm. Global alignment can be seeded using local alignment algorithm. Good for alignment the entire sequence. | *[http://bibiserv.techfak.uni-bielefeld.de/dialign/ DiAlign:] DNA-DNA Global Alignment Algorithm. Global alignment can be seeded using local alignment algorithm. Good for alignment the entire sequence. | ||
Revision as of 11:53, 10 August 2009
 | |
| Typical GEvo Analysis | |
| Software company | CoGe Team |
|---|---|
| Analysis Type | Compare multiple genomic regions for synteny and other forms of genome evolution |
| Working state | Released |
| Tools Utilized | blastn, tblastx, blastz, CHAOS, LAGAN, DiAlign 2 |
| Website | http://synteny.cnr.berkeley.edu/CoGe/GEvo.pl |
GEvo is CoGe's Genome Evolution Analysis tool, designed to visually compare genomic regions using both local and global alignment algorithms.
Contents
Introduction
The purpose of GEvo is to compare multiple genomic regions from any number of organisms using a variety of different sequence comparison algorithms in order to quickly identify patterns of genome evolution
Alignment Algorithms
Current GEvo can use:
- BlastZ: DNA-DNA Local Alignment Algorithm. Good for finding large regions of conserved sequence.
- BlastN: DNA-DNA Local Alignment Algorithm. Good for finding small regions of conserved sequence.
- TBlastX: Translated DNA-Translated DNA Local Alignment Algorithm. Good for finding small regions of divergent, but evolutionarily conserved, genomic sequence where protein translated sequence is more conserved than DNA sequence.
- Chaos: DNA-DNA Local Alignment Algorithm. Good for finding small regions of conserved sequence. Uses fuzzy matches so it can seed its alignment on small sequences than BlastN. However, it is slower than BlastN.
- DiAlign: DNA-DNA Global Alignment Algorithm. Global alignment can be seeded using local alignment algorithm. Good for alignment the entire sequence.
GEvo supports using Chaos, BlastN, and BlastZ for seeding DiAlign.
- Lagan: DNA-DNA Glocal Alignment. Using a hybrid alignment approach.
Overview
We have docs for this
Documentation
You should read this if you are confused.
Tutorials
We has them.
