AACon Web Service

From 721a650185138574d75e548b3e1f81113034ff45 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 4 Sep 2012 21:10:18 +0100 Subject: [PATCH] JAL-976 documentation for disorder, AACon, ClustalO services --- help/help.jhm | 2 + help/helpTOC.xml | 7 + help/html/webServices/AACon.html | 69 ++++++++ help/html/webServices/msaclient.html | 12 +- help/html/webServices/proteinDisorder.html | 241 ++++++++++++++++++++++++++++ 5 files changed, 325 insertions(+), 6 deletions(-) create mode 100644 help/html/webServices/AACon.html create mode 100644 help/html/webServices/proteinDisorder.html diff --git a/help/help.jhm b/help/help.jhm index 4288edc..e1bc443 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -18,6 +18,8 @@ + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index f594bd9..75aa6d2 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -20,10 +20,15 @@ + + + + + @@ -57,6 +62,8 @@ + + diff --git a/help/html/webServices/AACon.html b/help/html/webServices/AACon.html new file mode 100644 index 0000000..ea9b219 --- /dev/null +++ b/help/html/webServices/AACon.html @@ -0,0 +1,69 @@ + + + +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. +

+ + diff --git a/help/html/webServices/msaclient.html b/help/html/webServices/msaclient.html index ecca088..3e6c3cb 100644 --- a/help/html/webServices/msaclient.html +++ b/help/html/webServices/msaclient.html @@ -47,13 +47,13 @@ available: 'Edit Settings And Run ..' dialog box.

Alignment programs supported by JABAWS

ClustalW (version 2.0.12)
Mafft (version 6.713)
Muscle (version 3.7)
Tcoffee (version 8.14)

Alignment programs supported by JABAWS.
Versions shown are those bundled with JABAWS 2.01 - if you are using a different server, check its home page to find out which versions are provided.

Clustal Omega and Clustal W (version 2.0.12)
Mafft (version 6.8.57b)
Muscle (version 3.8.31)
Tcoffee (version 8.99)
Probcons (version 1.12)

Multiple Alignments of Sequences with hidden diff --git a/help/html/webServices/proteinDisorder.html b/help/html/webServices/proteinDisorder.html new file mode 100644 index 0000000..c12d2f6 --- /dev/null +++ b/help/html/webServices/proteinDisorder.html @@ -0,0 +1,241 @@ + + + +JABAWS Protein Disorder Prediction Services + + +

+ JABAWS Protein Disorder Prediction Services
+ The Web Services→Disorder menu in the alignment + window allows access to protein disorder prediction services provided + by the configured JABAWS + servers. Each service operates on sequences in the alignment to + identify regions likely to be unstructured or flexible, or + alternately, fold to form globular domains. +

+
+ Predictor results include both sequence + features and sequence associated alignment annotation rows. + Features display is controlled from the Feature Settings dialog + box. Clicking on the ID for a disorder prediction annotation row will + highlight or select (if double clicked) the associated sequence for + that row. You can also use the Sequence Associated option in + the Colour By + Annotation dialog box to colour sequences according to the results of + predictors shown as annotation rows. +
+
JABAWS 2.0 provides four disorder predictors which are described + below:
+
+
DisEMBL
+
IUPred
+
RONN
+
GlobPlot
+
+
+ DisEMBL + (Linding et al., 2003)
DisEMBL is a set of machine-learning + based predictors trained to recognise disorder-related annotation + found on PDB structures. +
+ + + + + + + + + + + + + + + + + + + + + +
Name Annotation type Description
COILS Sequence Feature &
Annotation Row + Predicts loops/coils according to DSSP definition[1].
Features mark range(s) of residues + predicted as loops/coils, and annotation row gives raw value for + each residue. Value over 0.516 indicates loop/coil. +
HOTLOOPS Sequence Feature &
Annotation Row + "Hot loops constitute a refined subset of COILS, + namely those loops with a high degree of mobility as determined from + Cα temperature factors (B factors). It follows that highly + dynamic loops should be considered protein disorder."
+ Features mark range(s) of residues predicted to be hot loops and + annotation row gives raw value for each residue. Values over 0.6 + indicates hot loop. +
REMARK465 Sequence Feature &
Annotation Row + "Missing coordinates in X-ray structure as defined by + remark465 entries in PDB. Nonassigned electron densities most often + reflect intrinsic disorder, and have been used early on in disorder + prediction."
Features gives range(s) of residues + predicted as disordered, and annotation row gives raw value for each + residue. Value over 0.1204 indicates disorder. +
+ +
+ [1]. DSSP Classification: α-helix (H), + 310-helix (G), β-strand (E) are ordered, and all other states + (β-bridge (B), β-turn (T), bend (S), π-helix (I), and + coil (C)) considered loops or coils. +
+ + +
+ RONN a.k.a. + Regional Order Neural Network
This predictor employs an approach + known as the 'bio-basis' method to predict regions of disorder in + sequences based on their local similarity with a gold-standard set of + disordered protein sequences. It yields a set of disorder prediction + scores, which are shown as sequence annotation below the alignment. +
+ + + + + + + + + + + +
Name Annotation type Description
JRonn[2] Annotation Row RONN score for each residue in the sequence. Scores above + 0.5 identify regions of the protein likely to be disordered.
+
+ [2]. JRonn denotes the score for this server because JABAWS + runs a Java port of RONN developed by Peter Troshin and distributed + as part of Biojava 3 + +
+
+ IUPred
IUPred + employs an empirical model to estimate likely regions of disorder. + There are three different prediction types offered, each using + different parameters optimized for slightly different applications. It + provides raw scores based on two models for predicting regions of + 'long disorder' and 'short disorder'. A third predictor identifies + regions likely to form structured domains. +
+ + + + + + + + + + + + + + + + + + + + + +
Name Annotation type Description
Long disorder Annotation Row Prediction of context-independent global disorder that + encompasses at least 30 consecutive residues of predicted disorder. + Employs a 100 residue window for calculation.
Values above 0.5 + indicates the residue is intrinsically disordered. +
Short disorder Annotation Row Predictor for short, (and probably) context-dependent, + disordered regions, such as missing residues in the X-ray structure + of an otherwise globular protein. Employs a 25 residue window for + calculation, and includes adjustment parameter for chain termini + which favors disorder prediction at the ends.
Values above 0.5 + indicate short-range disorder. +
Structured domains Sequence Feature Features highlighting likely globular domains useful for + structure genomics investigation.
Post-analysis of disordered + region profile to find continuous regions confidently predicted to + be ordered. Neighbouring regions close to each other are merged, + while regions shorter than the minimal domain size of at least 30 + residues are ignored. +
+
+ GLOBPLOT
Defines regions + of globularity or natively unstructured regions based on a running sum + of the propensity of residues to be structured or unstructured. The + propensity is calculated based on the probability of each amino acid + being observed within well defined regions of secondary structure or + within regions of random coil. The initial signal is smoothed with a + Savitzky-Golay filter, and its first order derivative computed. + Residues for which the first order derivative is positive are + designated as natively unstructured, whereas those with negative + values are structured.
+ + + + + + + + + + + + + + + + + + + + + + + + + +
Name Annotation type Description
Disordered Region Sequence Feature
Sequence features marking range(s) of residues with + positive dydx values (correspond to the #Disorder column from JABAWS + results)
Globular Domain + Sequence Feature Putative globular domains
Dydx Annotation row First order derivative of smoothed score. Values above 0 + indicates residue is disordered.
Smoothed Score
Raw Score + Annotation Row The smoothed and raw scores used to create the differential + signal that indicates the presence of unstructured regions.
These + are hidden by default, but can be shown by right-clicking on the + alignment annotation panel and selecting Show + hidden annotation + +
+
+ Documentation and thresholds for the JABAWS Disorder + predictors adapted from a personal communication by Nancy Giang, + 2012. +
+ + -- 1.7.10.2

Name	Annotation type	Description
COILS	Sequence Feature & Annotation Row +	Predicts loops/coils according to DSSP definition[1]. Features mark range(s) of residues + predicted as loops/coils, and annotation row gives raw value for + each residue. Value over 0.516 indicates loop/coil. +
HOTLOOPS	Sequence Feature & Annotation Row +	"Hot loops constitute a refined subset of COILS, + namely those loops with a high degree of mobility as determined from + Cα temperature factors (B factors). It follows that highly + dynamic loops should be considered protein disorder." + Features mark range(s) of residues predicted to be hot loops and + annotation row gives raw value for each residue. Values over 0.6 + indicates hot loop. +
REMARK465	Sequence Feature & Annotation Row +	"Missing coordinates in X-ray structure as defined by + remark465 entries in PDB. Nonassigned electron densities most often + reflect intrinsic disorder, and have been used early on in disorder + prediction." Features gives range(s) of residues + predicted as disordered, and annotation row gives raw value for each + residue. Value over 0.1204 indicates disorder. +