prionpartitioner.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


---  PRION PARTITIONER  ---

---  1)  Outline of Function ---

To read in 3 fasta files (where 2 files are subsets of the third),
and write 3 different fasta files so that each sequence only appears 
in ONE file.

Designed to be used in conjunction with Diana searches (originally for 
prions)

For example:

    file 1)  complete fasta file of prions in genome A
    
    file 2)  fasta file of prions in genome A that hit 
             to ANYTHING in genome B (subset of file1)
            
    file 3)  fasta file of prions in genome A that hit
             to PRIONS in genome B (subset of file2)
 
Will output files

    file A)  all prions UNIQUE to genome A (no hits to anything in genome B)
    file B)  all prions in genome A with homologue PRIONS in genome B
    file C)  all prions in genome A with non-prion homologues in genome B


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


prionPartitionInDir   directory in which to open infile file chooser

prionPartitionOutDir  default directory in which to write output files


---  3)  The User Interface  ---

fasta file of all prions in genome A
    File of all sequences.  the other two files are subsets of this file.
    
fasta file of prions in genome A that hit to:

    PRIONS in genome B 
        a subset of the sequences in the first file and the third file
        
    ANYTHING in genome B 
        also a subset of the sequences in the first file

select output directory
    directory to which all outfiles will be written

enter name of genome A
    The name of the genome from which the sequences in the infiles are taken

enter the name of genome B
    The name of the genome against which the sequences in the first infile
    were compared to create the 2nd and 3rd infiles


---  4)  Underlying Method   ---

  Takes 3 fasta files, and produce from them 3 different fasta files.
 
  FILES TO READ IN:
 
    file1)  complete fasta file of prions in genome A
    
    file2)  fasta file of prions in genome A that hit 
            to ANYTHING in genome B (subset of file1)
            
    file3)  fasta file of prions in genome A that hit
            to PRIONS in genome B (subset of file2)
 
 
  FILES TO OUTPUT: NO redundancy - each sequence appears in only one file
 
    file1)  all prions UNIQUE to genome A (no hits to anything in genome B)
    file2)  all prions in genome A with homologue PRIONS in genome B
    file3)  all prions in genome A with non-prion homologues in genome B