envsettings.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


---  ENVIRONMENT SETTINGS  ---

---  1)  Outline of Function ---


To hold paths to directories and executables used by the programs within genome explorer.

Paths to directories MUST NOT end with a file separator character (/ or \)


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


All of them - that's the point.


---  3)  The User Interface  ---


The parameters are grouped into program type to reflect the main program menu

Each program group tab contains another set of tabs to each individual program

GENERAL TIPS

Directory:  path to a real directory.  Do NOT end the path with "/" or "\"
	          
	   Input directories: generally control the directory in which a file 
	                      chooser first opens.
	                      
     Output directories: generally the default directory for outfiles.
                         Can often be changed in the gui for a particular program
      
     Temp directories: directory to which temporary files will be written.
                       Mostly these CANNOT be edited at run-time.  So set them here
                       to something sensible.

Filename:  name of a file (not a path).  Must only contain letters, numbers, '_'
           and '.' characters.  Often an extension is appended by the running program.
           
     Outfile Basename:  name will be incremented for each input file 
                        e.g. name_1.ext, name_2.ext

Extension:  extension to be added to an outfile name so that you recognise the file
            as created by a particular program

Executable:  path to an actual executable that will be called by genome explorer programs.
             These really need to point to working executables or nothing will work!
             

COMMON SETTINGS TAB     - for parameters used by more than one program

default directory
     Whenever a directory parameter is required by a gui or program, this directory is
     provided as a default.  If the desired parameter is not set, this directory will 
     be used instead.  MAKE SURE IT POINTS SOMEWHERE REAL!!
     
fasta line length
     number of residues per line of fasta output

html viewer executable
     all documentation is viewed via an html viewer. Ensure this points to a real
     executable or you won't get any help files, or any outfile links files

directory for html files of outfile links
     every program that produces outfiles provides an html file of links to all the
     outfiles it produced.  This makes it very easy for the user to view temporary
     files, or check that output is what they expected.
     Those files will be written to this directory
     
genome explorer documentation directory
     directory in which all genome explorer documentation is located



SEQUENCE SEARCH TAB
     
		parameters for:  residue search, diana, prion partition, extract seq name
		                 count sequences in fasta file and compare fasta files.


HOMOLOGY SEARCH TAB

    parameters for:  blast, blast parser, retrieve seq, homology search
                     and gene order matrix


HOMOLOGY ALIGNMENT TAB

    parameters for:  clustalw and the alignment editor


BUILD PHYLOGENY TAB
  
    parameters for:  phylip, chromtree, compare trees and view phylogenies


OTHER TOOLS TAB

    parameters for:  evolve
    
    
---  4)  Underlying Method   ---


see explanation in 'outline of function' section