geneordermatrix.txt

来自「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」· 文本 代码 · 共 80 行

***  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


---  GENE ORDER MATRIX  ---

---  1)  Outline of Function ---

 Class to convert RunHomologySearch output files into matrix files
 in Chromtree input format.
 
 Enables many files to be run consecutively without interaction from the user.
 
 Allows homology files to be corrupted by introducing errors in the data
 (deleting HomologyArray elements, forcing HomologyArray elements to hold inaccurate
 homolId or direction data).

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

matrixInDir directory in which to open the input file chooser

---  3)  The User Interface  ---

select homology files to run
     use the add / remove buttons to select a list of homology files 
     (files output by the Genome Explorer program 'Homology Search').

include unique sequences
     tick this checkbox to include unique sequences.  If it is unchecked, no 
     sequences unique to a single species will be included in the final gene
     order.  Unique sequences are removed *before* any interference is added.
     
alter homology data to make it inaccurate
     if this tool is being used to simulate missing or inaccurate data to 
     test phylogeny building programs, then tick this box and set the 
     inaccuracies

percentage of sequences that will randomly:
   a) be reassigned to a homology group
        causes this percentage of sequences to have their homologId changed
        to another one (that is already represented in the data set).
        To simulate inaccurate data and incorrect homology assignment.
   b) be deleted
        causes sequences to be deleted altogether to simulate missing data
   c) have their directions reversed
        causes sequences to have their directions reversed.  This situation
        is unlikely to happen in real data, but is here for completeness.
   d) be switched with their neighbour.  
        causes sequences to have their positions in the gene order moved by
        one position - sequences are literally switched with their neighbours.
        This simulates contigs being assembled in the wrong order.

---  4)  Underlying Method   ---

 Class to convert RunHomologySearch output files into matrix files
 in Chromtree input format.
 
 Enables many files to be run consecutively without interaction from the user.
 
 Allows homology files to be corrupted by introducing errors in the data
 (deleting HomologyArray elements, forcing HomologyArray elements to hold inaccurate
 homolId or direction data).
 
 Data corruption occurs in the following order
   1) all deletions
   2) all homolId reassignments
   3) all direction reversals
   4) all neighbour switches
   
 It is therefore possible for a unit to end up with it's homolId and direction changed