AliGraf - GeneBee Graphical Alignment Help

General options

Alignment title

Type in a title for this session for you to remember. This title used in the pictures.

Short name

Type in an alignment algorith name (Genebee, ClustalW, Manual...). This name placed at upper left corner of the pictures.

Picture options

Picture size

All images have same size. Width and height of the images may be set from 450 to 3000 and 200 to 10000 pixels, respectively. Defaults are 765 and "AUTO". When height set to "AUTO", the program selects the value itself (about 16 pixels per displayed sequence).

Coloring mode

Even - all column space are colored;
Sparse - every column is colored with respect to the column weight:
         less weight more space is left uncolored;
Very sparse - more space is left uncolored. So, important columns
              (with greater weight) are better seen.

Splitting block size

Long alignments can be splitted into several parts. You can select the size of one part in the range 50 to 500 letters.

Weight matrices

 Select a weight matrix to compute the column weights.
Defaults are Blosum62 for protein and DNA/RNA for nucleotide.

Picture types

An alighment can be presented in one or several graphical forms :
All groups - all letter groups are colored;
Max group at column - colored only letters of a maximum (dominant) group 
                      at every column;
Column values - a few statistical functions (column values): 
  - the number of letters in max group at the column,
  - the number of same letters at the column,
  - the number of groups at the column,
  - the weight of the column;
Column values (best-to-worst) - same functions but another ordering. 
                                That is in the range best to worst over X-axe.

Also you can get a picture when only selected groups are colored.

Color group type

AUTO - the program defines the molecular type of the source 
       alignment and selects respective group type;
Protein - protein groups will be used (see below);
Nucleotide - nucleotide groups will be used (see below);
You can select the color group type, protein or nucleotide, or leave it to the program (the type "AUTO") to decide which one should be used. There are the following protein letter groups: 
      1. _______A G _______________ 

      2. _______C _________________ 

      3. _______D E N Q B Z _______ 

      4. _______I L M V ___________ 

      5. _______F W Y _____________
 
      6. _______H _________________ 

      7. _______K R _______________ 

      8. _______P _________________ 

      9. _______S T _______________
 
     10. _______Others ____________
There are the following nucleotide letter groups: 
      1. _______A _________________ 

      4. _______C _________________ 

      6. _______G _________________ 
 
      4. _______T U _______________ 

      5. _______Others ____________

Add picture with selected groups

Select one or several groups to be colored in additional picture. You can get also the picture just with gaps without any groups colored (option "Gaps only").
Group set depends on selected group type.

Alignment

 The query alignment should be written in one-letter code (low or upper case) and can be divided to several strings. It have to be blank string between sequental batches and at the begining of every batch all sequence names should be repeated: 
KAG2_CAVPO    -----------------------------CGGVLVDPQWVLTAAHCIND--S---N
KAG_PIG       -----------------------------CGGVLVNPKWVLTAAHCKND--N---Y
PLMN_PIG      parvvggcvsiphswpwqislryryrgHFCGGTLISPEWVLTAKHC----------
TRYP_PIG      -----------------------nsgsHFCGGSLINSQWVVSAAHCYKS--R---I
UROK_PIG      -----------------------------CGGSLISPCWVVSATHCFINYQQKEDY

KAG2_CAVPO    QVKLGRHNLFEDEDTA-----QHFLVSQSVPHPDFN
KAG_PIG       EVGWLRHNLFENENTA-----QFFGVTADFPHPGFN
PLMN_PIG      ------------lekssspssykvilgaheeyhlge
TRYP_PIG      QVRLGEHNIDVLEGNE-----QFINAAKIITHPNFN
UROK_PIG      IVYLGRQTLHSSTHGEMKFEVEKLILHEDYSADSLA

Most important alignment rules and typical errors:

1. Different sequences should have different names.
2. Empty symbols aren't advisory inside sequence name.
3. Several blanks are advisory between sequence and its name.
4. Empty lines are mandatory inside parts of alignment.
5. Gap symbol must be '-'.
6. Beginning and finishing gaps are necessary.
Last updated: August 26, 2001.