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Importing and Coloring Sequence Alignments

The coloring macros allow to color a sequence alignement according to the properties of the amino acids. To do this, the sequence alignment has to be imported into an EXCEL worksheet or workbook in such a way that each amino acid occupies an individual cell of the worksheet.

Click the "HowTo" button for step by step instructions on how to import a sequence alignment into EXCEL and how to color it according to one of the predefined coloring schemes.


General Utilities:

AA_DefineColors defines the color map of an EXCEL workbook or worksheet to ensure that the alignment is colored as intended, independent of the version of EXCEL used. Run this macro before applying any of the coloring macros.

The following macros are all used in the same way: select the cells containing the date you want to process, then choose "Macro" from the "Tools" menu and start the appropriate macro

AA_Parse converts a text string in a single cell into individual characters in consecutive cells. You can select a range of cells within the same column. Do not select more than one column, cells to the right of this column will be overwritten by the parsed sequence. To parse sequences with more than 250 AA per line you have to cut them into smaller pieces during the fixed-format inport or by using the substring-function and process the pieces separatly

AA_Parse_3Letter converts a text string into tripletts of characters in consecutive cells, assuming one separation character, converting e.g. Amino acid sequences in 3-letter-code or nucleotide tripletts. You can select a range of cells within the same column. Do not select more than one column, cells to the right of this column will be overwritten with the parsed sequence.

AA_Convert_3to1 converts a sequence alignment from 3-letter code to 1-letter-code (for KABAT database), replaces the input triplett by the output letter => duplicate the worksheet before translating. Cells containing uninterpretable data or comment indicators are highlighted.

AA_Convert_NtoAA translates nucleotide code to 1-letter amino acid code. Replaces nucleotides with amino acids => duplicate the worksheet before translating. Requires worksheet "code" in AHo_macros.xls. Each cell has to contain one nucleotide triplet.

AA_SeqLength counts number of valid amino acid within the selected sequences. The result is placed in the column following the selected sequence block.

AA_CDR_Arrange counts number of valid amino acid within the selected rows, consolidates gaps and places them in the center of the sequence block, centering the consolidated gaps on a given sequence position.

Coloring Sequence Alignments:

AA_Empty Fills empty cells with the gap character "." and colors them black.

AA_Type colors a sequence alignment by amino acid type (color code)

AA_Hydropathy colors cells according to amino acid hydropathy (Parameters of Kyte+Doolittle, J. Mol. Biol. 157(1982)105-132) (color code)

AA_Charge colors the selected amino acids according to charge: acidic residues (Asp, Glu) are colored red, basic ones cyan (His) and blue (Lys,Arg)

AA_Cys highlights Cys residues in a sequence alignment. The macro can easely by changed to highlight any other amino acids

AAAAA Homepage Zürich University Dept. of Biochemistry Plückthun Group Annemarie Honegger

Last Modified by A.Honegger Wednesday, January 26, 2005