As a final note on mapping, it was found that duplicate mappings, using the same MAQ map command (with default parameters), and the same reads and reference data yielded slightly different results.
Marker order in groups was established using the "Calculate Map" command.
We used Maq's "map" command with default parameters, except when testing the bison reads using the "map" command's parameter "-m" (detailed below in the section, Calling single-base differences to the reference).
For another Cytoscape app to use any of these commands, it would need to call one of the Cytoscape TaskManagers and provide it org.cytoscape.command.CommandExecutorTaskFactory's createTaskIterator method with the appropriate argument map, command, and command namespace.
After an initial manual fitting using the program Chimera, the fit was further optimized using the "Fit in Map" command in Chimera (Pettersen et al, 2004).
In this way, they have introduced the Palm Menu, which directly maps commands or operations to different combinations of fingers and they have found that using finger chords has significant performance advantage.
For best performance, the user has to find the ideal queue-device mapping at command queue creation time, an effort that requires a thorough understanding of the underlying device architectures and kernels in the program.
If the current network is a logic network, before mapping this command performs structural hashing of the factored forms of the nodes (resulting in an AIG) followed by balancing (resulting in an AIG that is well-balanced for delay).
If the current network is a logic network, before mapping this command performs structural hashing of the factored forms of the nodes (resulting in an AIG) followed by balancing, which algebraically restructures the AIG for optimum delay measured using the number of logic levels of AND gates.
To construct consensus maps, the maternal maps and paternal were aligned based on the co-dominant markers (1 2 1, 1 1 1 1 and 1 1) and intercross markers (3:1), and then consensus maps were constructed by using JoinMap function "Combine Groups for Map Integration" command.
