chromtree.txt

比对算法的具体应用DNA序列分析 ——基因序列 ——基因表达调控信息 寻找基因牵涉到两个方面的工作 ： 识别与基因相关的特殊序列信号 预测基因的编码区域 结合两个方面的结果确定基因的位置和结构 基因表

***  GENOME EXPLORER HELP FILE  ***

To provide help on using the GUI, and information about how the programs run

Contents

1)  Outline of Function
2)  Parameters loaded from the .inf file (settings menu)
3)  The User Interface
4)  Underlying Method


---  CHROMTREE  ---

---  1)  Outline of Function ---

Chromtree generates trees or distance matrices from gene-order data.
See chromtree documentation for a full description of each available
method.

---  2)  Parameters loaded from the .inf file (settings menu) ---

chromtreeGeneOrderDir  directory in which to open gene-order file chooser

chromtreeOutDir        default output directory

chromtreeOutExt        extension for chromtree output files (.dist)     

chromtreeExeDir        path to directory in which chromtree executables live.
                       At the moment the only recognised executable is
                       segpall.exe.

chromtreeTempDir       DOS compliant directory to write temporary chromtree
                       input files.  No directory within it can have a name
                       of more that 8 letters. (D:/temp)

chromtreeTempFilename  DOS compliant filename for chromtree input files.  Must
                       have a name less than 8 letters long.  (chrom)

---  3)  The User Interface  ---

STANDARD TAB

select chromtree program to run
      At the moment the only option here is segpall.

select gene-order files to input
     add / remove paths to gene-order files

select output directory
     directory to which outfiles will be written

distance options:
ML distance from generated paths
ML distance from observed number of breakpoints
neighbour-pair distance
breakpoint distance

data options
data are unsigned integers
full tracking output

ML OPTIONS TAB

see chromtree documentation for details of the effect these options have 
on your chosen distance option.


---  4)  Underlying Method   ---


see explanation in 'outline of function' section