The program for finding pathways by tracking carbons is available as a jar file: CarbonSearch.jar The program currently requires a mysql database to access certain data, a mysqldump of this database can be downloaded here. Three sets of data files are also required to run the program: Mol files obtained from KEGG Cleaned RPAIR mappings from KEGG Cleaned reaction mappings based on RPAIR from KEGG To run the program (assuming you have Java installed): java -jar CarbonSearch.jar [input file] The input file contains all of the necessary information to run the program. It consists of a list of field names and field values separated by a tab. An example input file is available here.
| Description of the field names in the input file | |
|---|---|
| DBHOST | where the mysql database is hosted |
| DBPORT | port of the mysql database |
| DBNAME | mysql database name |
| DBUSER | mysql database user with access to the database |
| DBPASS | mysql password for the database user |
| MOLDIR | where the mol files are located |
| RPAIRDIR | where the cleaned RPAIR mappings are located |
| REACTIONDIR | where the cleaned reaction mappings are located |
| STARTCID | the KEGG compound ID for the start compound |
| TARGETCID | the KEGG compound ID for the target compound |
| K | value of K for Eppstein’s algorithm (usually set quite large) |
| NUMCARBON | number of carbons to conserve |
| DELTALENGTH | the number added to the shortest path length to determine the seed pathways, for example if the shortest path is of length 10 and DELTALENGTH is set to 4, then all pathways up to length 14 will be used |
| BRANCH | if set to 0, only find linear pathways, if set to 1, find branched pathways |
| NUMRETURN | the maximum number of pathways to return |
| OUTPUTDIR | where the output files (in dot format) will be written |