Hello Wenhe, Have you tried using our free Discovery Studio Visualizer?
http://accelrys.com/products/discovery-studio/visualization-download.php You can generate and color alignments using various properties like alignment similarity, chemical type, steric, and many others. In addition, you can select your own custom coloring for each property. I have attached a small screenshot of the view for your sample picture trying to match your coloring scheme. Cheers, Francisco Francisco Hernandez-Guzman, PhD, MBA Sr. Product Manager http://accelrys.com From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of WENHE ZHONG Sent: Thursday, February 02, 2012 9:32 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] off-topic: "special" format for multiple sequence (protein) alignment Dear members, Apologize for this off-topic question. I am looking for a protein sequence alignment tool which is capable to generate a particular output file similar to the attached format (please see the attached picture). I have been looking at some popular programs but none of them can show the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. King regards, Wenhe
<<attachment: sequence_alignment.jpg>>
