Display TMS Distribution in Multiple Sequence Alignment

Input:
Type a name of your file (optional)
ClusterW Options: MATRIX: Gap Open Penalty: Gap Extent Penalty:
Paste your file contents: Please paste the sequences in your file:

Display:
Help: Please paste all contents in your file and then press the 'click to draw' button below.    Each protein in the file must have a unique name.    Currently we only accept academic users. If you are blocked and you are actually an academic user, please contact xzhou@biomail.ucsd.edu and inform us of your server name.    After confirmation we will be happy to add you to our list for service.

Please note: Our sever is Unix based, so it will not accept such characters as - (dash) or white space. For example, while the name "Pab 12" or "Pab-12" is compatible with the Macintosh or Windows operating systems, it is not compatible with Unix, and will result in an error.

The number of TMS for each sequence is included inside the parenthesis after each protein name.    Because of our server limitation, there is a limitation about the amount of data each user can submit.    Our recommendation is to submit around 20 sequences each time.
Other:
About the program: This program first runs ClustalW to get the alignment file, then runs HMMTOP to get TMS positions and finally labels those TMS's in the alignment file. This Program was developed in Dr. Milton Saier's group. Please send questions to xzhou@biomail.ucsd.edu
ONLY ACADEMIC USAGE
About ClusterW: The ClustalW software used in this search was kindly provided by the European Molecular Biology Laboratory
About HMMTOP: The HMMTOP software used in this search was kindly provided by Dr. G.E. Tusnády with restrictions that only academic users can use this software.