An alighment can be presented in one or several graphical forms (picture types):
- all letter groups are colored; - colored only letters of a maximum group at every column; - colored only letters of selected groups; - 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; - same functions but another ordering. That is in the range best to worst over X-axe.
You can select the color group type, protein or nucleotide, or leave it to
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 ____________
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).
Every column can be colored evenly or with respect to column weight: less weight more space is left uncolored (sparse coloring).
Long alignments can be splitted into several parts. You can select the size of one part in the range 50 to 500 letters.
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