Conservation of the sequence according to HSSP

The Amino acid sequence conservation and reliability according to HSSP (7) data is presented here. The Evolutionary Pressure, calculated based on HSSP alignments, adequately prepared by BLUE STAR STING to be served as an input to Rate4Site (8) software, is also shown.

Placing the cursor above this element: pop-up area will show the position (sequence number and amino acid three letter code) for selected amino acid and the 4 numerical values for Conservation for given amino acid.
Left mouse click: no action
Right mouse click: on any of the "Conserv.(HSSP)" will generate following menu and actions:

A) "Temperature Factor X-Y Graphics" will produce following Java X-Y graphics (X= sequence number, Y= Relative Entropy) with the interactive possibilities described in dedicated HELP manual:

B) ConSSeq: This option invokes a ConSSeq component of BLUE STAR STING with its characteristic display. See more details about ConSSeq in its own help pages.



C) SeaView Multiple Sequence Alignment editor will show all the sequences used by HSSP in order to calculate consensus sequence and relative entropy.

D) TreeView Phylogenetic tree viewer will show all the relationship of sequences aligned and used by HSSP in order to calculate consensus sequence and relative entropy. Tree is calculated using ClustalW software. The input to ClustalW was the BLUE STAR STING especially prepared MSA, based on HSSP.

E) STING it "Evolutionary Pressure (HSSP)": This option generates structural presentation with color coding of the amino acids corresponding to the JPD color coding for this particular parameter. Amino acids are presented in CPK rendering. This feature is exceptionally useful as it allows to a user to inspect within the structure, a parameter describing a sequence conservation.

F) STING it "Relative Entropy100 (HSSP)": This option generates structural presentation with color coding of the amino acids corresponding to the JPD color coding for this particular parameter. Amino acids are presented in CPK rendering. This feature is exceptionally useful as it allows to a user to inspect within the structure, a parameter describing a sequence conservation. "Relative Entropy 100" indicates that only the first 100 (most similar)sequences from the HSSP MSA were used in order to calculate Relative Entropy.

G) STING it "Relative Entropy (HSSP)": This option generates structural presentation with color coding of the amino acids corresponding to the JPD color coding for this particular parameter. Amino acids are presented in CPK rendering. This feature is exceptionally useful as it allows to a user to inspect within the structure, a parameter describing a sequence conservation.

H) STING it "Reliability": This option generates structural presentation with color coding of the amino acids corresponding to the JPD color coding for this particular parameter. Amino acids are presented in CPK rendering. This feature is necessary if a user wishes to evaluate the reliability of the calculated conservation parameter. If all sequences used for the MSA are present at this particular position in the sequence, then the reliability is equal to 1 (100). If say only 15 sequences are showing an amino acid at this particular position in the sequence, while HSSP have collected 100 sequences in total, then the reliability is equal to 0.15(15). For cases where only up to 5 sequences were identified by the HSSP for calculation of the relative entropy, we decided to attribute value of ZERO for the reliability.

At the top part of the figure below we show the JPD Relative Entropy raw. Below it, there is a portion of the actual HSSP file, showing in the last column the data which we read in into JPD: the RELENT.