- The Multi-Harmony (a.k.a. Sequence Harmony and Multi-Relief, or SHMR) service (Brandt, Feenstra and Heringa, 2010) available - from the Analysis sub-menu of the alignment window's web - services menu provides a method for the identification of significant - patterns of sub-family variation amongst the columns of an - alignment. -
-
- Instructions for use
The service requires a
- protein sequence multiple alignment that has been sub-divided into
- groups containing at least two non-identical protein sequences. An
- easy way to create groups is to use the built-in neighbour-joining or UPGMA tree
- routines to calculate a tree for the alignment, and then click on the
- tree to subdivide the alignment.
-
- The SHMR service operates on the currently selected visible region(s) - of the alignment. Once submitted, a job progress window will display - status information about your job, including a URL which allows you to - visit the status page on the - IBIVU SHMR server. -
-When the job is complete, Jalview will automatically open a new - window containing the alignment and groups that were submitted for - analysis, with additional histograms added portraying the SHMR scores - for each column of the sub-grouped alignment.
-
- If you use this service in your work, please cite :
Brandt,
- B.W.*, Feenstra, K.A*. and Heringa, J. (2010) Multi-Harmony: detecting
- functional specificity from sequence alignment. Nucleic
- Acids Res. 38: W35-W40. (* joint first authors)
-
- Note: The Multi-Harmony service is implemented with a prototype of Jalview's RESTful - web service client introduced in Jalview 2.7. A few bugs remain in this prototype, which we intend to fixed in version 2.7.1. - -
+ Functional residue analysis with Sequence Harmony and + Multi-Relief ++ The Multi-Harmony (a.k.a. Sequence Harmony and Multi-Relief, or + SHMR) service (Brandt, Feenstra and Heringa, + 2010) available from the Analysis sub-menu of the + alignment window's web services menu provides a method for the + identification of significant patterns of sub-family + variation amongst the columns of an alignment. +
+
+ Instructions for use
The service requires
+ a protein sequence multiple alignment that has been sub-divided into
+ groups containing at least two non-identical protein sequences. An
+ easy way to create groups is to use the built-in neighbour-joining or
+ UPGMA tree routines to calculate a tree for the alignment, and
+ then click on the tree to subdivide the alignment.
+
+ The SHMR service operates on the currently selected visible + region(s) of the alignment. Once submitted, a job progress window + will display status information about your job, including a URL + which allows you to visit the status page on the IBIVU SHMR + server. +
+When the job is complete, Jalview will automatically open a new + window containing the alignment and groups that were submitted for + analysis, with additional histograms added portraying the SHMR + scores for each column of the sub-grouped alignment.
+
+ If you use this service in your work, please cite :
+ Brandt, B.W.*, Feenstra, K.A*. and Heringa, J.
+ (2010) Multi-Harmony: detecting functional specificity from sequence
+ alignment. Nucleic
+ Acids Res. 38: W35-W40. (* joint first authors)
+
+ Note: The Multi-Harmony service is + implemented with a prototype of Jalview's RESTful web service client + introduced in Jalview 2.7. A few bugs remain in this prototype, + which we intend to fixed in version 2.7.1. + +