X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2FAACon.html;h=5cec67d69bde614d163a596d93cd60e9fc8e2798;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=8652e0f7829ea1b54facd4cac7df08ffd53a4ef0;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git diff --git a/help/html/webServices/AACon.html b/help/html/webServices/AACon.html index 8652e0f..5cec67d 100644 --- a/help/html/webServices/AACon.html +++ b/help/html/webServices/AACon.html @@ -1,70 +1,73 @@ + --> AACon Web Service - AACon Alignment Conservation Calculation Service -

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. -

+ AACon Alignment Conservation Calculation Service +

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. +