The JABAWS AACon service implements 17 different conservation - scores for protein sequence alignments.
-- The majority of these scores were described by Valdar in 2002 (Scoring - residue conservation. Proteins: Structure, Function, and - Genetics 43(2): 227-241. PubMed or - available on the Valdar - Group publications page), but the SMERFs score was developed later - and described by Manning et al. in 2008 (BMC - Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51). -
-
- Enabling and disabling AACon calculations
When
- the AACon Calculation entry in the Web
- Services→Conservation is ticked, AACon calculations will be
- performed every time the alignment is modified. Selecting the menu
- item will enable or disable automatic recalculation.
-
- Configuring which AACon calculations are performed
- The Web Services→Conservation→Change AACon
- Settings ... menu entry will open a web
- services parameter dialog for the currently configured AACon server.
- Standard presets are provided for quick and more expensive
- conservation calculations, and parameters are also provided to change
- the way that SMERFS calculations are performed.
AACon
- settings for an alignment are saved in Jalview projects along with
- the latest calculation results.
-
-
- Changing the server used for AACon calculations
- If you are working with alignments too large to analyse with the
- public JABAWS server, then you will most likely have already
- configured additional JABAWS
- servers. By default, Jalview will chose the first AACon service
- available from the list of JABAWS servers available. If available, you can switch to
- use another AACon service by selecting it from the Web
- Services→Conservation→Switch Server submenu.
-
The JABAWS AACon service implements 17 different conservation + scores for protein sequence alignments.
++ The majority of these scores were described by Valdar in 2002 + (Scoring residue conservation. Proteins: Structure, + Function, and Genetics 43(2): 227-241. PubMed or available on the Valdar Group publications page), but the SMERFs score was + developed later and described by Manning et al. in 2008 (BMC Bioinformatics 2008, 9:51 doi:10.1186/1471-2105-9-51). +
+
+ Enabling and disabling AACon calculations
+ When the AACon Calculation entry in the Web
+ Services→Conservation is ticked, AACon calculations will be
+ performed every time the alignment is modified. Selecting the menu
+ item will enable or disable automatic recalculation.
+
+ Configuring which AACon calculations are performed
+ The Web Services→Conservation→Change
+ AACon Settings ... menu entry will open a web services parameter dialog for the currently configured AACon
+ server. Standard presets are provided for quick and more expensive
+ conservation calculations, and parameters are also provided to
+ change the way that SMERFS calculations are performed.
AACon
+ settings for an alignment are saved in Jalview projects along with the latest calculation results.
+
+
+ Changing the server used for AACon calculations
+ If you are working with alignments too large to analyse with the
+ public JABAWS server, then you will most likely have already
+ configured additional JABAWS
+ servers. By default, Jalview will chose the first AACon service
+ available from the list of JABAWS servers available. If available,
+ you can switch to use another AACon service by selecting it from the
+ Web Services→Conservation→Switch Server
+ submenu.
+