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Welcome to the RAPTOR GUI page. This page has been developed for those interested in seeing what RAPTOR has to offer, but without having to install the software for a demo evaluation. If this page encourages you to test out the software for yourself we have two options, RAPTOR Online and the downloadable demo version.

If you care to read more about fold recognition, check out our Fold Recognition/Protein Threading Basics page.

The RAPTOR software is streamlined for user ease. We start off with a task pane, so the logical thing to do is load a query sequence. The sequence can be obtained from any directory accessible by your computer. To load this, under the file menu, click "Load File". Alternatively you can click the Load Sequence HotKey

. In this case, we are going to run just one sequence, 2acy.seq. RAPTOR operates by running sequences with the base tag "SEQ" and produces output files with the base tag "XML".

Now we see the query sequence, 2acy.seq, in its entirety.

When we click the Run Sequence HotKey,

or select "Run Selected" from the Run drop down menu. The Configuration pane comes up and explains what we want to do with RAPTOR and where to put the results.

For this short example we are just going to go through the basic configuration.
We see the different types of tests we can run, No Core, NP Core and IP.

The next section in this pane describes the 3D application and pretty much just asks us to identify where the modeling program can be accessed from.
For users with ICM Pro software, RAPTOR can produce input files and here is where you can direct them to be placed.

The output directory is exactly what it sounds like. Once RAPTOR has completed the sequence it will produce an XML file and store it in a specified location.

Lastly, if we want to obtain raw output files from RAPTOR, we can, just click the box.

Click Run and the sequence will be threaded to each template in the structure library.

The first pane that opens up is the PSI-BLAST Profile pane. This displays which residues are conservative. The dark colours mean the residues are very conservative and the light colours correspond to less or non-conservative residues.

The Secondary Structure pane located next to the PSI-BLAST Profile pane represents loops (in blue), helixes (in red) and beta strands (in yellow).
Here we see such relevant details as the Amino Acid sequence (AA) and the Predicted Secondary Structure (PHD). The third row displays the confidence (Rel) score which is a number corresponding to each residue between 0 and 9.
0 being poor, 9 being optimal.

In the third pane, Ranking by Score (of the Templates), displays the evaluations of each test we performed. When you click a test method folder, each result within it is displayed. Here you can find such relevant factors as E values, specially generated Z scores and you can also find the alignment at the bottom.

The last pane is the Alignment pane, which allows us to compare between the different methods of testing performed. For example, we can observe the top 5 alignments for one method (see Figure 4.1) or we can compare any two alignments from any two methods at the same time.

The last thing we should note here, is that by clicking on the View link, we can call a separately installed modelling program to display the predicted tertiary structure and even display the tertiary template structure.
Click and drag your mouse around inside this new window in order to have the image rotated in its three dimensional fold.

This page was designed to simply give users and potential users a quick impression of what RAPTOR is capable of producing. Other features not discussed on this page, but possible with RAPTOR include; running multiple sequences, advanced configuration and simple navigation to relevant sequences within the NCBI website, just to name a few.

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Approach Product Line Online Server Tech Support Request Prices Download Demo Benchmarks User Comments User Research	Superior protein structure prediction Software RAPTOR RAPTOR GUI (Graphical User Interface) Welcome to the RAPTOR GUI page. This page has been developed for those interested in seeing what RAPTOR has to offer, but without having to install the software for a demo evaluation. If this page encourages you to test out the software for yourself we have two options, RAPTOR Online and the downloadable demo version. If you care to read more about fold recognition, check out our Fold Recognition/Protein Threading Basics page. The RAPTOR software is streamlined for user ease. We start off with a task pane, so the logical thing to do is load a query sequence. The sequence can be obtained from any directory accessible by your computer. To load this, under the file menu, click "Load File". Alternatively you can click the Load Sequence HotKey . In this case, we are going to run just one sequence, 2acy.seq. RAPTOR operates by running sequences with the base tag "SEQ" and produces output files with the base tag "XML". Now we see the query sequence, 2acy.seq, in its entirety. When we click the Run Sequence HotKey, or select "Run Selected" from the Run drop down menu. The Configuration pane comes up and explains what we want to do with RAPTOR and where to put the results. For this short example we are just going to go through the basic configuration. We see the different types of tests we can run, No Core, NP Core and IP. No Core: Dynamic Programming used to align the query sequence to a template. NP Core: Dynamic Programming used to align the query sequence to the template, but the template is parsed as a series of cores connected by loops. IP: Integer Programming used to align the query sequence to the template. Pair-wise interactions are treated rigorously The next section in this pane describes the 3D application and pretty much just asks us to identify where the modeling program can be accessed from. For users with ICM Pro software, RAPTOR can produce input files and here is where you can direct them to be placed. The output directory is exactly what it sounds like. Once RAPTOR has completed the sequence it will produce an XML file and store it in a specified location. Lastly, if we want to obtain raw output files from RAPTOR, we can, just click the box. Click Run and the sequence will be threaded to each template in the structure library. The first pane that opens up is the PSI-BLAST Profile pane. This displays which residues are conservative. The dark colours mean the residues are very conservative and the light colours correspond to less or non-conservative residues. The Secondary Structure pane located next to the PSI-BLAST Profile pane represents loops (in blue), helixes (in red) and beta strands (in yellow). Here we see such relevant details as the Amino Acid sequence (AA) and the Predicted Secondary Structure (PHD). The third row displays the confidence (Rel) score which is a number corresponding to each residue between 0 and 9. 0 being poor, 9 being optimal. In the third pane, Ranking by Score (of the Templates), displays the evaluations of each test we performed. When you click a test method folder, each result within it is displayed. Here you can find such relevant factors as E values, specially generated Z scores and you can also find the alignment at the bottom. The last pane is the Alignment pane, which allows us to compare between the different methods of testing performed. For example, we can observe the top 5 alignments for one method (see Figure 4.1) or we can compare any two alignments from any two methods at the same time. The last thing we should note here, is that by clicking on the View link, we can call a separately installed modelling program to display the predicted tertiary structure and even display the tertiary template structure. Click and drag your mouse around inside this new window in order to have the image rotated in its three dimensional fold. This page was designed to simply give users and potential users a quick impression of what RAPTOR is capable of producing. Other features not discussed on this page, but possible with RAPTOR include; running multiple sequences, advanced configuration and simple navigation to relevant sequences within the NCBI website, just to name a few.