PURPOSE: The user specifies an sequence alignment file and a reference sequence found in the alignment. The protocol then performs a pairwise alignment between each sequence in the alignment file and the reference sequence. The sequences are sorted by the percent identity so that the sequence with the highest percent identity to the reference is listed first. Note, the Percent Sequence Identity that is reported does not include gaps.
The Intermediate folder contains one pir file for each input sequence aligned to the reference sequence. The Output folder contains an alignment 'all.pir' which is a concatenation of all the pairwise alignments. The reference sequence is listed first and then is every other sequence in the alignment i.e. sequence 1 is the reference and sequence 2 is the sequence that has the highest percent identity to the reference, sequence 3 is the reference and sequence 4 is the sequence with the second highest sequence identity to the reference etc.

USAGE: This protocol can be launched from both the Discovery Studio and Pipeline Pilot clients. To install in Discovery Studio only, go to the Protocol Explorer, right-click over the folder you want to add the protocol to, choose Import, navigate to the location of the Align123_to_Reference.xml file and enter it as the File Name.

REQUIREMENTS: Discovery Studio Component Collection.

DISCLAIMER: This custom protocol is compatible with Discovery Studio 2.5.5 and Pipeline Pilot server version 7.5.2 (SES). It is provided "as is" and is NOT supported by Accelrys nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.