clustalw.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


---  CLUSTALW  ---

---  1)  Outline of Function ---

Runs clustalw with the same command line parameters for a whole list of files

(rewrites infile to tempfile in temp directory before it runs clustalw.  This
prevents a whole host of DOS naming problems.)

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

clustalInDir         directory in which to open infile file chooser

clustalOutDir        default directory in which to write output files

clustalProfileDir    directory in which to open profile file chooser

clustalExePath       path to clustalw executable

clustalTempDir       path to directory in which to write temp files
                     this MUST be a DOS compliant directory, and very 
                     simple.  e.g. D:/temp or the like.
                     
clustalTempFilename  VERY simple filename that is DOS compliant (clustal.tmp)


---  3)  The User Interface  ---

align a file of sequences / convert a file from one type to another
     Radio buttons to indicate what clustalw is to be used for

select input file
     add / remove files from the list box using the add / remove buttons
     Input files could be of any format accepted by clustalw, but at the moment it
     only takes fasta...

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

gap open penalty (default 10.0)
     the penalty clustalw assigns when opening a gap.  The default parameters are for 
     aligning homologous sequences of similar lengths.

gap extension penalty (default 0.2)
     the penalty clustalw assigns when extending a gap.  The default parameters are for 
     aligning homologous sequences of similar lengths.

select input type
     select the input file type if all alignments are of the same type (dna or protein).
     If alignments are a mix of types, then leave as "default" and clustalw will 
     figure it out.  "default" is always the safe option.

select output type
      clustalw will output in several different formats.  Select one from the list
      or use the default (clustalw).
      If you are moving directly to phylogeny generation, choose 'phylip'.  
      'gde' is much the same as fasta, but with gaps in - the sequences are NOT interleaved.

select first / second profile (optional - not available in DOS version)
     clustalw accepts profiles for some alignments - see clustalw documentation for
     more information

select input file type (not available in DOS version)
      choose protein or dna to reflect the type of sequences being aligned.

select output sequence order (not available in DOS version)
      aligned: outputs the sequences with the least conforming last
      input:   outputs the sequences in the same order as the input file

select case for gde output file (not available in DOS version)
      gde (a similar format to fasta, but with gaps) can be output in upper or lower case

switch print clustal seq nos (not available in DOS version)
      option to print sequence numbers when the output format is clustalw (.aln extension).
      'on' prints sequence numbers, 'off' doesn't.


---  4)  Underlying Method   ---


Each input file in turn is copied to the tempfile in the temp directory to enable primitive
DOS based clustalw to find it.  Clustal then writes an outfile to this directory, which is
copied to the user's directory of choice before they know what's happening.

Several GUI options are not available in the DOS version of genome explorer because clustalw
DOS command line is limited to 119 characters.

Runs clustalw with the same command line parameters for a whole list of files