YOC is a whole genome alignment tool designed for collinear genomes.
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OverlapChainer
fasta_files
.gitignore
LICENSE
README.md
YOCchain2alignments.pl
computeCoverage.awk
genomeLength.awk
inverseGenome.awk
runOC.csh
runYOC.csh
runYass.csh
testInversedGenomes.awk
yass_blast2chainer.cpp

README.md

YOC

YOC is a whole genome alignment tool designed for collinear genomes. It has been developed by Raluca Uricaru (LIRMM/LaBRI).

Usage

The main script to run is runYOC.csh, which takes:

  1. the first genome to compare in fasta format
  2. the second genome to compare in fasta format
  3. the E-value for YASS similarity search
  4. the overlap ratio for OverlapChainer

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_output : YASS intermediary results in .yass, .yass1, and .mat formats

results : simple chaining result with coordinates only (.chn), chaining result with alignments (.chn_yass), and coverage statistics

Installation

  1. Compile the translator : make yass_blast2chainer
  2. Compile the java code (from the root dir): javac -sourcepath OverlapChainer/src -d OverlapChainer/bin OverlapChainer/src/overlapChainer/*.java OverlapChainer/src/tests/*.java
  3. Get Yass v1.14: http://bioinfo.lifl.fr/yass/download.php and link it (or copy it) into the root folder under the name: yass_1.14
  4. Enjoy ;)

Requirements

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)

are required.

YOC works on Apple Mac OS X and Linux systems.

Output

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).