ClustalW Alignment

From: jprocter Date: Thu, 16 Jun 2005 17:42:10 +0000 (+0000) Subject: more doco. X-Git-Tag: Release_2_0~4 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c30bcb5bc195374ef89916a1c39e4812fa93bf4c;p=jalview.git more doco. --- diff --git a/help/html/webServices/clustalw.html b/help/html/webServices/clustalw.html new file mode 100755 index 0000000..3258494 --- /dev/null +++ b/help/html/webServices/clustalw.html @@ -0,0 +1,31 @@ + +ClustalW Alignment + +

ClustalW Alignments

ClustalW is a program for multiple sequence alignment. It works +with both DNA and protein sequences, and can also perform profile +profile alignments to align two or more multiple sequence +alignments.

+Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994)
+CLUSTAL W: improving the sensitivity of progressive multiple +sequence alignment through sequence weighting, position specific gap +penalties and weight matrix choice.
+Nucleic Acids Research 22 4673-4680 +

There are two versions of this alignment function, which will operate +on the selected region, if any, or the whole sequence set:

Calculations→Web Service→Clustal +Alignment..
+Aligns using the clustalW program, ignoring any gaps in the submitted +sequence set. +
Calculations→Web Service→Clustal +Realign..
+Submits the sequences with existing gaps to clustalW, which will +preserve existing gaps and re-align those regions which are not optimal. +

+ + diff --git a/help/html/webServices/jnet.html b/help/html/webServices/jnet.html new file mode 100755 index 0000000..93c13d8 --- /dev/null +++ b/help/html/webServices/jnet.html @@ -0,0 +1,85 @@ + + +JNet Secondary Structure Prediction + + +JNet Secondary Structure Prediction +

+Secondary structure prediction methods attempts to infer the likely secondary +structure for a protein based on its amino acid composition and +similarity to sequences with known secondary structure. The JNet +method uses several different prediction methods and decides on the +most likely prediction via a jury network.
+

Cuff J. A and Barton G.J (1999) Application of enhanced multiple +sequence alignment profiles to improve protein secondary +structure prediction Proteins 40 502-511

+The function available from the Calculations→Web +Service→JNet... menu does two different kinds of +prediction, dependent upon the currently selected region:

If nothing is selected, and the displayed sequences appear to +be aligned, then a JNet prediction will be run for the first +sequence in the alignment, using the current +alignment. Otherwise the first sequence will be submitted for prediction. +
If +just one sequence (or a region on one sequence) has been selected, +it will be submitted to the automatic JNet prediction server +for homolog detection and prediction. +
If a set of sequences are selected, and they appear to be aligned, +then the alignment will be used for a Jnet prediction on the +first sequence selected in the set (that is, the one +that was first clicked on). +

The result of a JNet prediction for a sequence is a new annotated + alignment window:

+The sequence for which the prediction was made is the first one in the +alignment. If a sequence based prediction was made then the remaining +sequences in the alignment are the aligned parts of homologs which +were used to construct a sequence profile for the prediction. If the +prediction was made using a multiple alignment, then the original +multiple alignment will be returned, annotated with the prediction. +

+The annotation bars below the alignment are as follows:

Lupas_21, Lupas_14, Lupas_28
+Coiled-coil predictions for the sequence. These are binary +predictions for each location.
JNETSOL25,JNETSOL5,JNETSOL0
+Solvent accessibility predictions - binary predictions of 25%, 5% +or 0% solvent accessibility.
JNetPRED
+The consensus prediction - helices are marked as red tubes, and +sheets as dark green arrows.
JNetCONF
+The confidence estimate for the prediction. High values mean high +confidence. prediction - helices are marked as red tubes, and +sheets as dark green arrows.
JNetALIGN
+Alignment based prediction - helices are marked as red tubes, and +sheets as dark green arrows.
JNetHMM
+HMM profile based prediction - helices are marked as red tubes, and +sheets as dark green arrows.
jpred
+Jpred prediction - helices are marked as red tubes, and +sheets as dark green arrows.
JNETPSSM
+PSSM based prediction - helices are marked as red tubes, and +sheets as dark green arrows.
JNETFREQ
+Amino Acid frequency based prediction - helices are marked as red tubes, and +sheets as dark green arrows.
JNETJURY
+A '*' in this annotation indicates that the JNETJURY was invoked +to rationalise significantly different primary predictions.

+ + diff --git a/help/html/webServices/jnetprediction.gif b/help/html/webServices/jnetprediction.gif new file mode 100755 index 0000000..3f827d9 Binary files /dev/null and b/help/html/webServices/jnetprediction.gif differ diff --git a/help/html/webServices/msaws.html b/help/html/webServices/msaws.html new file mode 100755 index 0000000..627fa65 --- /dev/null +++ b/help/html/webServices/msaws.html @@ -0,0 +1,65 @@ + + +Multiple Sequence Alignment Web Services + + +

Multiple Sequence Alignment Web Services

+ +

+Jalview +

+ClustalW +BLAh + +

+BLAh + +

+Muscle + + + diff --git a/help/html/webServices/muscle.html b/help/html/webServices/muscle.html new file mode 100755 index 0000000..58b29bc --- /dev/null +++ b/help/html/webServices/muscle.html @@ -0,0 +1,16 @@ + +Muscle Alignment + +

Muscle Alignments

Muscle is a program for the alignment of many protein sequences.

+Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high +accuracy and high throughput
+Nucleic Acids Research 32(5), 1792-97.

+This alignment method is applied to the selected region, if any, or +the whole sequence set when the Calculations→Web +Service→Muscle Alignment... menu is selected. +

+ +