The SAAP database may be searched for single nucleotide polymorphisms by entering an accession number. By default, the program will guess the type of search being attempted. If a more specific search is required however, clicking on the Options show/hide links will display a further two pull down menus.

Using the ID Type menu, it is possible to search explicity for entries in SAAP by the following accession/ID numbers:

• Human Genome Variation Database (HGVBase)
• Single Nucleotide Polymorphism Database (dbSNP)
• EMBL Nucleotide Sequence Database or GenBank
• Gene Symbol
• Protein Data Bank
• UniProt Knowledgebase

Searching on HGVBase or dbSNP will take you to the SAAP database entry for that SNP while searching on the other terms will return a page with a table of SAAP entries found for the search term. The results can be filtered using the Display pull down menu to return either: all the entries found in SAAP, only the validated entries, silent or non-silent mutations. Ticking the checkbox at the bottom of the form will set the search to return only entries with structural data (ie PDB entries).

Data from the following selected locus specific mutation databases has been incorporated into SAAP:

• ADAbase: Mutation registry for Adenosine Deaminase Deficiency
• HAMSTeRS: The Haemophilia A Mutation, Structure, Test and Resource Site
• Hereditary deficiency in human Glucose-6-phosphate dehydrogenase.
• IARC TP53 Mutation Database
• OMIM - Online Mendelian Inheritance in Man
• ZAP70base: Mutation registry for autosomal recessive ZAP70 deficiency

The SAAP database may be searched for disease causing mutations by entering an accession number. By default, the program will guess the type of search being attempted. If a more specific seach is required however, clicking on the Options show/hide links will display a further two pull down menus.

Using the ID Type menu, it is possible to search explicitly for entries in SAAP by the following accession/ID numbers:

• Mutation ID (For instance, from Online Mendelian Inheritance in Man (OMIM))
• Gene Symbol
• Protein Data Bank
• UniProt Knowledgebase

Searching on these accession/ID numbers will return a page with a table of SAAP entries found for the search term. The table can be ordered by either Mutation ID number or by residue number. Ordering by residue number can be useful when searching on either UniprotKB or PDB. Clicking the checkbox at the bottom of the form will set the search to return only entries with structural data (ie PDB entries)

Protein structures in the SAAP database can be displayed by clicking on the RasMol icon:

Rasmol is a free molecular structures visualisation program originally developed by Roger Sayle running under the Linux, Windows and Mac operating systems. The program can be downloaded from www.openrasmol.org. An online RasMol manual is availible from www.openrasmol.org/doc/rasmol.html.


Configuring Browsers to run RasMol

A helper script is required to to launch Rasmol.

For unix systems create a file named 'start_rasmol_script.com' containing the following two lines:

#!/bin/csh
xterm -e rasmol -script $1

and make it executable using the command:

chmod +x start_rasmol_script.com

For windows create a file named 'start_rasmol_script.bat' containing the following two lines:

cd /D C:\TEMP
"c:\Program Files\rasmol\raswin.exe" -pdb %~1

There are two possible approaches to setting-up your browser to deal with RasMol:

Begin by clicking the RasMol icon. If this results in the browser asking which application should be should be used to open this filetype then:

1. Use the Choose button to to choose the 'start_rasmol_script.com' file.
2. Click on the 'Always use this application' checkbox.

Alternatively:

1. Choose Preferences or Settings (the name varies in different browsers) from the pulldown menus to bring up a window for changing the settings on your browser
2. Find and click on the Applications (or Helper Applications) option
3. Choose New and fill in the form as follows:-
Description: Rasmol Script
• MIME Type: application/x-rasmol
• Suffixes: (leave blank)
4. Use the Choose button to select 'start_rasmol_script.com' as the application to use with this file type.
5. Click on OK