• Accession Number (universally valid, one or more per entry)

• Title (usually similar in between databases, one line of description)

• Reference (the literature reference or location of the lab that produced the sequence)

• Sequence (always starting with position 1, even in DNA).

(Some data which serve administrative purposes, such as section information or dates of creation or updating, are not listed.)

• Features of the sequence (reading frame coordinates, protein functional motifs, etc.)

If you want to retrieve an entry from the database, it is important to decide what type of query will be most effective:

• Query by reference, author, sequence name, etc.: This is a search in the annotation. The programs described in this chapter perform this type of search after having obtained the keywords to be searched. The result will be a list of entries which match the keywords exactly.

The following sections describe GCG software as well as additional software which may not be part of your installation.

Databases available at Basel University include:

 
Database name          GCG name            contents   
----------------------------------------------------------------  
EMBL + Updates     
GENBANK + Updates   
(GB as exclusion set)  GENEMBL:            all DNA databases (1)  
  
SWISSPROT              SWISSPROT:          most proteins (2)  
PIR International      PIR:                most proteins  
PATCHX + PIR           MIPSX:              MIPS merged database (3)  
  
NEW entries of EMBL    XEMBL:              EMBL new entries (4)   
UPDATED entries EMBL   XXEMBL:             EMBL updated entries (5)  
  
GENBANK update excl.   GB_NEW:             GENBANK exclusion (6)  

1) The definition of GENEMBL can vary. Depending on the location, you can use either GENBANK with an exclusion set of EMBL data not found in GENBANK, or vice versa (e.g., in Basel). Depending on whether you are connected to a network which is used to update data on a periodic basis, the GENEMBL set may include also daily updates.

2) containing weekly updates

3) PATCHX is updated quarterly and includes the previous release of SWISSPROT, an automatic translation of EMBL, and some other databases.

4) The definitions vary. XEMBL, EM_NEW, EMBL_DAILY, GB_NEW, XSWISS, SW_NEW, PIR4, etc. are names that denote the character of the preliminary entries.

5) This is a Basel-specific item. The main purpose of this database is to find new data in the annotation, as updates rarely include changes in the sequence. In order to have the main EMBL database show not too many entries in FASTA runs, the XXEMBL database is not included in the usual GENEMBL set.

ATLAS> bases

The next command activates all databases:

ATLAS> bases *

To search for titles, type

ATLAS> find

and for help

ATLAS> help

View Data on the Screen

$ typedata /ref

ATLAS> show

$ fetch

 
FETCH copies GCG sequences or data files from the GCG database  
into your directory or displays them on your terminal screen.   
  
FETCH what sequence(s) ?  genembl:pbr322 	  
  
pbr322.syn  
  

ATLAS> copy

If you want to see a list of sequence names which can be used in ATLAS later on, use

ATLAS> list

The SRS program has an in-built copy option. Select [O] to set options and [E] to list entries, then [H] to save buffer or [N] to write names.

The ENTREZ program has an in-built copy option. Select the <save> button.

Example:

 
  
$  MAIL   
Mail> send   
To: SMTP%'netserv@embl-heidelberg.de'        
Subj: help  
<CTRL> <Z>  
Mail> quit  
$  
  

 
  
New mail on node YOGI from SMTP%"netserv@embl-heidelberg.de"  
  

 
  
You have 1 new mail message.  
  

 
  
$  mail   
You have 1 new mail message.  
Mail> last  
From:SMTP%"netserv@embl-heidelberg.de"  
Subj: Automatic reply......  
Mail> extract/noheader  
File: mail.dat  
Mail> delete  
Mail> quit  
$  
  

The 'EAN' Program in VMS

The following example assumes that you have setup and configured 'ean' correctly. (This is an automatic procedure if you start the program for the first time.)

Example:

 
  
$  ean  
> comp  
To: netserv@embl-heidelberg.de  
Subj: help  
<CTRL> <Z>  
send   
options?  send  
> quit  
$  
  

Find Sequences in the Databases with 'gopher' (via network)

$ LYNX

After you have started 'lynx', you should see a screen full of text. Use the cursor keys to select an option and hit <RETURN> to activate the field.

Getting Started

'mosaic' Users

First, open an extra 'mosaic' window to work in. You can do this by clicking on the <clone> button at the bottom of the screen. Then, pull down the <File> menu, select <Open URL> and type in one of the addresses listed above to get to the main SRS page.

'netscape' Users

First, open an extra 'netscape'n window to work in. You can do this by pulling down the <File> menu and selecting <New Window>. (You can also hit <ALT><N> on the keyboard.) Then, click on the <open> icon in the first row and type in one of the addresses listed above to get to the main SRS page.

Example: Searching Databases

• Searching the Sequence Databases: Selection

  You should now see a full page query form. At the top, there is a list of the sequence databases that are installed at the site you are visiting. The highlighted boxes show which database(s) are selected for searching. Normally, only SWISSPROT is selected. You can now change the selection. The next time you come back to this form you will see that your latest selections are still there. This is not easy over the Web, but SRS uses a few tricks. You may see a lot of extra numbers creeping into the "Document URL" line at the top of the screen. That is how SRS is keeping a record of which session you are in so it can save and recall your options.

  For the purpose of this startup tutorial, unselect SWISSPROT and activate EMBL.

• Searching the Sequence Databases: Keywords

  The next four lines of the query form allow you to specify what you want to search in the sequence databases. Left to the input box there is a selection button. Click on the first selection button (which originally says "AllText") and change it to "Organism" by moving the pointer down before you release the mouse button. In the box type the word "sacc" (we are going to search EMBL for all entries that contain a sequence from "sacch*"). To start the query, i.e., to search the half-million entries of EMBL, simply click on the <DO-QUERY> button.

• Result Inspection

  You should now see more than 8000 EMBL entries listed on the screen. Click on one of them (EMBL:entryname) to read the text. Each of these entries has "saccharomyces" somewhere in the organism definition.

• More Detailed Results

  Go back to the query form (use the <Back> button at the bottom of the screen) and take a look at the scrolling region that says "Id", "Accession", "Date", "Definition", and so on. Select "Definition" and then click on the <DO-QUERY> button again. Instead of just showing you the entry names, SRS will now show you the definition lines as well.

• Linking to PROSITE

  We would like to know which of the sequences found before have a known protein motif. Look at the top line and select the [S+L] field. You will get a page which shows all databases which possibly have information associated to the query you just performed. Select "PROSITE" by highlighting the box and click on the <DO-LINK> button.

• Searching a Specific Motif

  You can try to search for "calcium binding" in the page you just visited. This may, however, not be feasible as only chunks of sequences are displayed. Therefore, use the link [Top] at the top of the page to get back to the main SRS page. There, select the <Search a library linked to sequence libraries> button.

• Querying a Non-Sequence Database

  You will again get a full page query form. The first line shows the database you have selected at the previous step (PROSITE). Since non-sequence databases may be very different, you can only query one database at a time. The next four lines allow you to specify what you want to search in the databases. Left to the input box there is a selection button. Click on the first selection button (which originally says "ID") and change it to "Definition" by moving the pointer down before you release the mouse button. In the box type the word "calcium". Do the same with the second box and type the word "binding". In this way, we are going to search PROSITE for all entries that contain the words "calcium" AND "binding" in the definition. To start the query, i.e., to search the PROSITE database, simply click on the <DO-QUERY> button.

• Result Inspection

  Three entries or more should show up. You can now combine these with the previous query for "saccharomyces". To do so, select [QueryManager] at the top of the page.

• Combining Queries

  The page you see now is perhaps the most difficult page in SRS, but also the most powerful one. You can now "map" the result of the "calcium binding" question to the more than 8000 entries from the query for "saccharomyces". Go to the expression window and type

  Q3 > Q1

  Submit the query with the <DO-QUERY> button. You will get all saccharomyces DNA sequences which are known to have a calcium-binding motif.

This is only a short introduction. Use the system extensively to practice.