diana.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


---  DIANA  ---


---  1)  Outline of Function ---


Defined Interval Amino-acid Numerating Algorithm.

Allows user to search for a minimum number of the search element within a 
particular sequence window (length of amino acids / nucleotides within a sequence).

Produces an output file for each input file, of all sequences which meet the 
entered criteria.  The output file will be in fasta format.

The search element can be:

 a) a number of different nucleotides / amino acids to be searched for individually
    but counted cumulatively
    (e.g. search for Q and N:  in 10 residue window yNabggQNyN: cumulative score: 4)

 b) a number of different nucleotides / amino acids to be searched for individually
    but counted independently
    (e.g. search for Q and N:  in 10 residue window yNabggQNyN: Q score:1, N score: 3,
     highest overall score: 3)
 
 c) a number of strings searched for individually and counted cumulatively
    e.g. search for GGY and YQQ: in 10 residue window aaaGGYQQgg:
         GGY score: 1, YQQ score: 1, cumulative score 2
    however
         search for GG and QQ in 10 residue window aaGGGygQQg
         GG score: 1, QQ score: 1, cumulative score 2.
         because when GG is found, the search continues from where that 'hit' ends...
 
 d) a number of string searched for individually and counted independently
    As for c) but only the highest score will count
  


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


fastaLineLength  number of characters per line of fasta output (80)

dianaInDir       directory in which to open the infile file chooser

dianaOutDir      default directory to which all output files will be written

dianaOutfileExt  file extension for all outfiles (.di_out.fasta)


---  3)  The User Interface  ---


fasta files to search
     Use the add / remove buttons to add / remove files to / from the list box.
     All files displayed in the list box will be searched (independently) when 
     the program is run.

select output directory
     select the directory to which all output files will be written

use infile name as outfile basename
     tick this check box to use the name of the file being searched as the basename
     for the outfile of sequences that meet criteria.  The file extension
     dianaOutfileExt (as set in the settings panel) will be added.

select a name for output fasta file
     enter the basename for output files - this will be incremented for each infile
     and the file extension dianaOutfileExt will be added.  
     e.g.  outfile_1.diOut, outfile_2.diOut etc

match min quantity
     match a minimum number of residues in a window of a specific size.
     
match min percentage
     match a minimum percentage of residues in a range of window sizes.
     
min number of matches in window
     number of matches per window - if cumulative search, total number of all matches
     must equal or exceed this number if sequence is to be a 'hit'.  If NOT cumulative
     one individual search must equal or exceed this score for sequence to be a hit.
     e.g. search for Q and N in 10 residue window, min number matches = 5
          yNQbggQNyN  
          Q score: 2, N score: 3
          cumulative score: 5 therefore hit
          OR
          individual max score: 3, therefore not a hit
     
min window size (residues)
     the minimum number of residues in the search window (only applicable when a percentage
     search is being performed)

max window size (residues)
     the maximum number of residues in the search window (for a percentage
     search) or the fixed window size (for a minimum quantity search).

report progress every x sequences
     reads the fasta files to be searched in blocks of this many sequences to prevent
     memory problems.  Reports progress to the screen every time a batch finishes.

count all residue string hits cumulatively
     tick this box to count hits cumulatively, as described in the 'outline of function' 
     section of this document

strings to search for (; separated)
     enter the strings to search for if you do not want to search for individual 
     nucleotides or amino acids.  Upper/lower case is irrelevant as all data is
     converted to lower case before comparisons are made

dna sequence / protein sequence / enter text
     radio buttons enable the different components for entering searches

nucleotide / amino acid check boxes
     tick the boxes of ALL residues you want to search for


---  4)  Underlying Method   ---


 Code for DIANA (Defined Interval Amino acid Numerating Algorithm).
 
 This class has additional functions that allow it to search for single elements,
 or strings of letters.
 
 ***
 
 FUNCTION
 
 read in a fasta file of protein sequences
 set a 'window size' in which to scan for a set of amino acids
 set the amino acids to scan for
 set a cut off number of key amino acids that must be found in the window to be interesting
 scan each possible window of each sequence for the key amino acids
 
 fasta file is read in 'batches' of sequences - to avoid hitting the memory ceiling
 
 ***
 
 ASSUMPTIONS
 
   1) that the input file is in FASTA format where '>' character indicates the start
      of a protein name
   2) that ALL characters in a sequence (except blank spaces) represent residues
      and should therefore be counted in length-of-protein counts, even if they
      do not represent a single specific residue
 
 ***
 
 ALGORITHM
 overall form of the diana part of this program
 
   1) get array of names and corresponding array of protein sequences
   2) determine average key aa per window (string of windowLength consecutive amino acids in a protein)
   3) look at all possible windows and find those rich in key aas
   4) output list of all sequences with key aa rich regions, and max key-aa-per-window value
 
 ***