Database functions of DNAMAN allow users to well organize DNA and protein sequences for different subjects.
Choosing the Database | Manager command to open the Database Manager dialog box. There are five functions in database management: selecting a database as the default database, creating a new database, deleting a database, changing the password of a database, and listing all records in a database.
Selecting a database
Click a database name to select it as the default database, then click the Exit button. All database related functions in DNAMAN are performed with the default database.
Creating a new database
Click the New button to open a New Database dialog box.
1) Database name
A database name consists of 8 or fewer letters. Do not use space or dot in the names.
2) Database Type
Select the DNA option to create a DNA database. Select the Protein option to create a protein database.
3) Password
The password ensures the security of database. If you want to delete the database, or add or erase a record of the database, DNAMAN will ask you to identify the password. Thus, a user can protect his or her database from others for modification. However, any user can retrieve records and information in a database without password.
It may not be necessary to have the password for some databases. When you are creating a database, click OK without giving a password to turn off the security.
Deleting a database
You can delete a database by clicking the Delete button and all records in the database will be lost.
Changing a password
You can change the password of a database.
1.Select a database as the default database.
2.Click the Password button.
3.Clicking the Password button opens a Password dialog box.
4.DNAMAN will ask you to type old password, enter and confirm new password.
5.Click OK to validate your change.
You may turn on or off the security of a particular database with this function.
Listing all records of a database
Press the Show All Records button to display all records of the default database. You may print out the list using the File | Print menu.
Choosing the Database | Edit Record command opens the DNAMAN Database dialog box. There are two ways of adding sequences to the database. Clicking the Add File button to add files and the Add Channel button for sequences in channels. Password is required if the database is protected. After entering the correct password, you can add a sequence file into the default DNA or protein database.
The initial “ORIGIN” is required for retrieving a DNA or protein sequence file from a disk. For the sequence without the initial, you can simply add the “ORIGIN” in the beginning of the sequence, and then save it (see the section IV.3). Example:
SEQ EXAMPLE1: 886 bp;
ORIGIN
1 TTTGACTGCC ACTTCCTCGA TGAAGGTTTT ACTGCCAAGG ACATTCTGGA
51 CCAGAAAATT AATGAAGTTT CTTCTTCTGA TGATAAGGAT GCCTTCTATG
101 TGGCAGACCT GGGAGACATT CTAAAGAAAC ATCTGAGGTG GTTAAAAGCT
The information relating to this new record is shown in seven fields:
- Sequence Name
- Definition
- Keywords
- Source
- Reference
- Memo
- CDS (coding region)
GenBank files have the ORIGIN initial. If one file contains more than one DNA or protein sequence; all these sequences will be added automatically into the default DNA or protein database as separate records.
Choose the Database | Edit Record command to open a dialog box. Select the record name you want to delete from the Sequence List box, then click the Delete button to erase the record and its related information.
The information relating to a specific record can be edited. In the Sequence List box, all records are listed in alphabetical or record order. The number following each record name indicates record ID. The record number is automatically assigned by DNAMAN. Therefore, you may have the same name for different records.
If a large number of sequences are stored in a database, it may be difficult to find out. In this case, you may use the sorting function to decrease the listing number. There are four sorting keys: Name, Definition, Keywords and Source. In any one of these boxes, type either a partial or the full content, then click the Show list button to start sorting.
After editing a record, click the Save button to save the modification.