YOC is a whole genome alignment tool designed for collinear genomes. It has been developed by Raluca Uricaru (LIRMM/LaBRI).
The main script to run is
runYOC.csh, which takes:
- the first genome to compare in fasta format
- the second genome to compare in fasta format
- the E-value for YASS similarity search
- the overlap ratio for
Use case example:
./runYOC.csh fasta_files/CP000412_GR.fsa fasta_files/CR954253_GR.fsa 10 10
The results are generated in two folders:
: YASS intermediary results in
: simple chaining result with coordinates only (
.chn), chaining result with alignments (
.chn_yass), and coverage statistics
- Compile the translator :
- Compile the java code (from the root dir):
javac -sourcepath OverlapChainer/src -d OverlapChainer/bin OverlapChainer/src/overlapChainer/*.java OverlapChainer/src/tests/*.java
- Get Yass v1.14: http://bioinfo.lifl.fr/yass/download.php and link it (or copy it) into the root folder under the name:
- Enjoy ;)
To run YOC,
- any version of tcsh, awk, Perl and a C compiler
- Java at least 1.6 (should work with minor adaptations downto 1.4)
YOC works on Apple Mac OS X and Linux systems.
YOC produces several result files, as follows:
.yass file (generated by YASS with -d 2 option), which gives information for every local similarity fragment (e.g., coordinates, length, identity percentage, alignment length, mismatches, gaps openings, E-value, ...). See YASS manual page for more details.
.yass1 file (generated by YASS with -d 1 option), which gives the alignment for each fragment. See YASS manual page for more details.
.mat file (obtained from the .yass file) gives the number of exact matches in each fragment and its coordinates.
.chn file (generated by OverlapChainer) gives those fragments that were taken in the chain, among the ones contained in the .mat file (the .chn format is similar to .mat format).
.chn_yass file (obtained from the .chn and the .yass1 files) gives the same fragments as in the .chn file, together with their alignments (the .chn_yass format is similar to .yass1 format).