Manual

Scientific DataBase Maker (SciDBMaker)

Release v1.1: Manual

SciDBMaker is stand-alone software that allows the extraction of protein data from the Swiss-Prot database, sequence analysis comprising physicochemical profile calculations, homologous sequences search, multiple sequence alignments and the building of new and more specialized databases. It compiles information with relative ease, updates and compares various data relevant to a given protein family and could solve the problem of dispersed biological search results.

Sommaire

1. User interface presentation. 1

2. Data input 3

3. Data treatment 5

3.1. Entry manipulations. 5

3.2. External programs parameters. 6

3.3. Sequence homology search using BLAST. 6

3.4. Multiple sequence alignments (MSA) using Clustalw v2.0. 7

3.5. Tree visualization using TREEVIEW... 8

4. Data output 8

4.1. Data saving, printing. 8

4.2. Database creation. 8

 


1. User interface presentation

      

1. Find text window                  2. Sequence edit window         3. Properties window

          

4. Blast window                         5. Alignment window

 

   

4. Database connector window            5. Desktop explorer window

 

2. Data input

Menu: File, open

Menu: Tools, Import SwissProt entry

 

New document, or add new sequence:

3. Data treatment

3.1. Entry manipulations

Add, remove: please see toolbar. Shortcuts are enabled (press “del” key to delete).

Edit sequence:  - Menu, Edition, edit sequence.

- Go to edit peptide sequence window

- right click into sequence entry

Entry properties: please see Properties window

For “PDB Entry”, “Other databases”, “References” columns: you may right click to find a toolstrip menu, which links to web sites, for each information.

Columns preferences: Menu: tools, display preferences. Here you may choose information’s to be extracted or calculated. “All columns” button permits the reset to all available information’s.

3.2. External programs parameters

Menu: Tools, External programs parameters

3.3. Sequence homology search using BLAST

Please select sequences to be blasted from the sheet. If you do not select rows, all sequences will be prompted for blast.

Please go to Blast Window.

Results will appear in a new web page window.

You should select homologous entries and press “retrieve” button. By default, entries will be retrieved to a new document. You may choose retrieve them to an existing document. By pressing “home page” button the blast search result page will be reloaded. You may click into present links to navigate and to view entries information’s (on NCBI web site).

3.4. Multiple sequence alignments (MSA) using Clustalw v2.0

Or Menu: Tools, ClustalW sequence alignment

MSA result window:

Alignment result may be saved as row text (Save button, or Menu: File, save)

3.5. Tree visualization using TREEVIEW

Window should appear automatically after finishing ClustalW alignment job. SciDBMaker capture a TREEVIEW session. You will then be able to fully use TREEVIEW. When launching more than TREEVIEW session, a warning message from this software will appear. Please close previous trees windows before starting a new alignment.

4. Data output

4.1. Data saving, printing

You may save sequence in fasta format, Excel sheet (“.xls”) or to database file (XML “.xml”, MysQL “.sql”, Access”.mdb”). Alignment may be saved to a row text (“.aln”).

Please click into save button or go to Menu: File, save.

You may also save only selected rows. Menu: Edit, export selected rows.

For printing, you may choose rows or all (default). Menu: File, Print preview; and Print.

4.2. Database creation

Menu: Tools, Database connector. Or Database connector window (docked right).


 

List bases: available databases list.

List tables: available tables list.

Open table: open requested table

Create requete: Before doing this, you should tape a name for the table. Generate a requete table for current document.

Do requete: will execute this requete on the database server.

When modifying data, you may save modification by pressing “save” button