seqaligneditor.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
 
 
 ---  GENE ORDER MATRIX  ---
 
 ---  1)  Outline of Function ---
 
     The Multi Sequence Alignment Editor tool reads in an aligned sequence file (such as 
     those written by clustalw or read by phylip programs) and displays it on the screen. 
     The display arranges sequences in rows, one row per sequence, so that all corresponding 
     character positions align in columns.  The user is permitted to insert and delete gaps 
     in the sequence, but may not alter the actual letters, or the order in which they appear.
     
     Background colours are pre-set for dna and protein sequences to aid in the alignment 
     process.  A GUI has not yet been implemented to allow the user to define their own 
     colour scheme, though the underlying code was written to accommodate this extension. 
     
    The editor displays sequences with identical lengths; if loaded sequences have differing
    lengths, the editor adds gap characters to the end of short sequences before displaying
    them.  The editor was designed to aid manual editing of computationally aligned sequences,
    and does not perform any alignment itself. However, several features assist the user 
    in locating and aligning particular regions of sequence using `search' and `insert gaps'
    functions.  
    These functions are particularly useful when sequences are known to align over a very 
    short region (e.g. a primer site, or a span identified in a BLAST report) and the 
    computational alignment is wildly inaccurate.  
    
    Several formats of file can be opened (fasta, gde, clustalw aligned, phylip) and saved 
    (fasta, gde, phylip), so the editor can be used as a format conversion tool.  
    Phylip format restricts the length of each sequence name to a maximum of ten characters.
    Sequence name editing is therefore implemented so that the user can ensure the first ten 
    characters of each name are unique before saving in phylip format.
    

 ---  2)  Parameters loaded from the .inf file (settings menu) ---
 
 alignEditorInDir  directory in which to open "file open" file chooser
 
 ---  3)  The User Interface  ---
 
 To select a column: click on the star above the column.
 To select a sequence: click on the name of the sequence.
 To insert gaps: click in the place you want to insert gaps, hit the space
                 bar or dash key.  A gap will be inserted.  To insert gaps
                 in more than one sequence simultaneously, select several
                 sequences by clicking on their names, and insert a gap in
                 one of them - the others will get gaps automatically.
                 To lock a column (and only insert gaps in front of it, 
                 thereby not disturbing the alignment beyond the selected 
                 column) click on the star above the column you want to lock.
 
 ** FILE MENU **
 
 Open - open an alignment file
 
 Save As - save as fasta (with no gaps), gde (like fasta, but with gaps), phylip
           (requires first 10 letters of each name to be unique)), clustalw.
           To save as a text file formatted to your exact specifications, use
           the Export function.
 
 Save - saves a file in the same format as it was opened in.  Beware if you opened
        a fasta file with no gaps!
 
 Close - closes the current file.  Has no record of whether it was changed since the
         last save, so reminds you that any changes will be lost.
 
 Print - opens the print preview window.  This allows you to format your sequence 
         to your exact specifications before printing (or exporting to a text or
         image file)
 
 Export - opens the print preview window.  This allows you to format your sequence 
         to your exact specifications before exporting to a text or
         image file (or printing).
 
 ** EDIT MENU **
 
 Edit sequence names - allows sequence names to be edited.  The sequence window is 
                       effectively disabled while this checkbox is ticked.  Don't 
                       forget to untick it when you have finished editing!
 
 Change sequence order - allows you to change the order in which your sequences
                         appear in the window (and in all saved files).
 
 Crop beginning of sequence to selected column - crops the beginning of all sequences
                         so that the first letter of every sequence is the one in the
                         selected column.  (select a column by clicking on the star
                         above it.)
 
 Crop end of sequence to selected column - crops the end of all sequences
                         so that the last letter of every sequence is the one in the
                         selected column.  (select a column by clicking on the star
                         above it.)
 
 Undo crop end - undoes that last "crop end" command.
 
 Undo crop beginning - undoes the last "crop beginning" command.
 
 Invert selected sequences - only applicable to dna sequences.  Reverses the order of
                             the nucleotides and replaces each one with its base
                             pairing partner (A-T and C-G).  Write the inverted sequence
                             below the original sequence in the display.  (Select sequences
                             by clicking on their names.)
 
 Remove selected sequences - Removes the selected sequences from the alignment.  There is 
                             no undo function for this, so take care!  (Select sequences
                             by clicking on their names.)
 

 ** COLOUR MENU **
 
 Protein text - colours sequence text according to clustalw groups.
 
 DNA text - colours sequence text so that each base has a different colour. 
 
 Protein background - colours sequence background according to clustalw groups.
 
 DNA background - colours sequence background so that each base has a different colour.
 
 Plain text - no colours at all.
 

 ** TOOLS MENU **
 
 Search for selected string
       Searches for the selected string (if one is selected in the sequence viewer) or
       allows you to input a sequence to search for.  
       
       search for inverse - search for the inverse of the selected sequence.
       
       ignore dashes in hits - will ignore gaps when searching.
       
       use selected - writes the currently selected sequence into the "search for" 
                      text box.
       
       search - searches for the given sequence from the first letter of the first
                sequence.  Appends the results to the results panel.
                
       search again - searches from the end of the last hit.  Appends the results
                      to the results panel.
       

 Insert /  Delete gaps
 
       Choose the sequence in which you want gaps to be inserted.  If this sequence
       name is currently selected, gaps will be inserted into all sequences whose 
       names are also selected.
       
       Choose whether to insert or remove spaces.
       
       at column - the column at which spaces will be inserted or removed
       
       Choose whether to align columns or insert/delete a particular number of spaces.
       Choosing to align columns simply allows the program to calculate how many spaces
       to insert / remove, based on the columns you need to align.  This option is 
       provided to enable you to easily align areas of sequence that the "search for 
       selected string" function has indicated are the same.
       
       Alternatively:
       
       Choose to close all the gaps in a sequence between the given columns.
       You need to choose where those gaps will be moved to (to keep all sequences
       the same length).  This can be the end or beginning of the sequence, or the
       end or beginning of the region from which gaps are being removed.
       
       All results are appended to the results panel.

 
 Compare seq for similarity
    
       Choose the region of sequence to compare.  Absolute position indicates the
       column numbers displayed in the viewer.  Selecting a sequence and giving
       start and end positions will ignore any gaps.
       
       Clicking "use selected" will use the absolute start and end positions of any
       region of sequence currently selected in the viewer.
       
       All sequences will be compared to all other sequences over the specified region.
       Perfect matches (where two compared letters are identical) are recorded.
       
       Results appended to the results window show the number of perfect matches for
       each sequence pair, the total number of residues compared, and the percentage
       (100 * perfect matches / total residues).
       
 
 ** ALIGN MENU **
 
 Run clustalw - runs clustalw on the current alignment.  Asks whether you want to save your
                alignment with no gaps before running clustalw.  This is recommended as a 
                better alignment will be achieved.  If you have already saved it with no gaps,
                ignore this question.
 
 ---  4)  Underlying Method   ---


see explanation in 'outline of function' section