residuesearch.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


---  RESIDUE SEARCH  ---

---  1)  Outline of Function ---

Program to search all the sequences in any number of fasta files, for any
number of search strings.

Complex output detailing how many times each search string occurs in
each sequence is written to the screen, and a simpler parseable output is
written to a file.  The single output file details the results of all the string
searches, grouped by search file.  Values are character separated and suitable
for import into excel.


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

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

resSearchInDir       directory in which to open the infile file chooser 
                
resSearchOutDir      default directory to which all output files will be written
                 
resSearchOutfileExt  file extension for all outfiles (.resSearch.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

select a name for outfile
     enter the name of the output file
     the file extension resSearchOutfileExt will be added.  
     Only one output file is produced, with output grouped by infile


semi-colon separated list of strings
     enter the search strings as a semicolon separated list.  Each string will be
     searched for individually, and a set of results produced.

select a character to separate the fields in the outfile
     for easy loading into a spreadsheet the fields are delimited by a character.
     Choose one from the drop down list


---  4)  Underlying Method   ---

Program to search all the sequences in any number of fasta files, for any
number of search strings.

Complex output is written to the screen, and a simpler parseable output is
written to a file.  The single output file details the results of all the string
searches, grouped by search file.  Values are character separated and suitable
for import into excel.

All search strings are searched for independently, and have their own output.
All searches are run on one file, before the next is loaded.
To prevent memory problems, only the number of sequences specified in
ResidueSearchParameters.reportProgressEvery are loaded into memory at any one time.

Output to screen:

	1) total number of sequences in fasta file
	2) total number of residues in fasta file
		 for each search string:
	3) total number of times that search string occurred in the sequences in the current fasta file
	4) number of sequences in which the search string occurred at least once
	5) list mapping number of times the search string appeared in a single sequence,
		 to the number of sequences with exactly that many hits:
				number of sequences with 0 hits=2553
				number of sequences with 1 hits=1632
				number of sequences with 2 hits=936

Output to file:

For each file:
 1) search filename
 2) total number of sequences in the file
 3) total number of residues in the file
 4) for each search string:
 
		a) total number of hits
		b) number of sequences with at least one hit
		c) maximum number of hits per sequence
		d) minimum number of hits per sequence (>0)
		e) mode number of hits per sequence