EMBL-Search
Version 2.0 - April 1992

Apple Macintosh Database Retrieval Software for EMBL Sequence Databases on CD-ROM

Copyrights

EMBL-Search and this documentation are copyrighted (© 1992 by European Molecular Biology Laboratory, EMBL, Heidelberg) and all rights are reserved.

EMBL-Search may be freely copied and redistributed without prior permission, provided that the software and the documentation are always bundled together, in whole and unchanged. EMBL-Search may not be sold or offered for sale, or bundled with another product offered for sale, without prior consent, in writing, from EMBL. These rules do not restrict the use of EMBL-Search, even if the results are of commercial value.

The software or the source code may be modified for personal use. Modified versions of the software or source code may not be given away without permission by EMBL.

The software is delivered on an “as is” basis. EMBL makes no warranties, either express or implied, regarding the software’s quality, its performance, or its fitness for any particular purpose. In no event will EMBL be liable for any special, consequential, indirect or similar damages, including any loss of data arising out of the use or inability to use the software or any data supplied therewith.

Introduction

EMBL-Search is a database retrieval software product for the Apple® Macintosh® computer. It enables a range of queries to be performed on the EMBL Nucleotide and the SWISS-PROT Protein Sequence databases on the CD-ROM provided by the EMBL Data Library in order to identify and extract entries from these databases.

This on-line help is a considerably stripped down version of the full user manual.

Technical Support

If you have problems installing or operating the software, or have any questions in respect to functionality please contact the EMBL Data Library and provide the following information:
•    The version number of EMBL-Search (as displayed
      on the “About EMBL-Search” screen).
•    A detailed description of your problem.
•    A profile of your Macintosh hardware, system 
      software and configuration.

Here’s how to contact the EMBL Data Library:

The EMBL Data Library
European Molecular Biology Laboratory
Postfach 10.2209
W-6900 Heidelberg
Germany

Telefax:        +49–6221–387 519
Telephone:    +49–6221–387 258
Electronic mail:    Datalib@EMBL-Heidelberg.DE
Communication by electronic mail is preferred.

The Query Window

This is the main window of EMBL-Search and used to enter and start database queries.

A database query is composed of up to five subqueries which are connected by a logical (Boolean) AND or OR operator selectable from a set of buttons.
Search strings are entered into the text edit boxes of this dialog. The commands Cut, Copy, Paste and Clear from the Edit menu can be used for editing search strings. To move from one box to the other use the Tab key or simply click with the mouse into the box you want to move to. The current text insertion point is marked by a blinking vertical bar (I-beam).

A subquery applies to a certain field in the database. This field can be chosen for each subquery individually from the set of popup menus at the right side of the query window next to each text box.

EMBL-Search assists the user in constructing queries by offering an index browser tool. To enter the index browser position the text insertion point into one of the text edit boxes, choose a database field from the corresponding popup menu and click the Browse Index button. The use of the index browser is described in detail below.

The database to be searched is specified by clicking one of the buttons in the lower left corner entitled EMBL or SWISS-PROT.

The query is executed by clicking the Search Database button. If the query yields no hits, an alert box appears and notifies the user. Otherwise a result window opens showing the hits found in the database. In the present version queries cannot be interrupted.

Queries can be stored to disk using the Save and Save As commands from the File menu. Saved queries can be used again later with the Open Query command, even with different releases of the CD-ROM.

Note: EMBL-Search checks whether query files that it attempts to read in are compatible with the currently installed CD-ROM.

The Clear Query button empties all text edit boxes in a query window and resets default values for database, logical operator and database fields.

The Duplicate Query command from the Edit menu opens a new query window which is an exact copy of the current one. This option is useful to establish different threads of a query. One can use the Duplicate Query command to get a copy of a query, modify and execute it, and can then easily return to the starting point to try a different strategy.

  Constructing Queries

All databases which can be used with EMBL-Search consist of different fields. Each field carries specific and well-defined information. The fields available in the EMBL and SWISS-PROT databases and the line types used to represent them in the flat file distribution format are described in the databases’ user manuals which you can find on the CD-ROM.

The EMBL-Search program uses index files which are supplied on the CD-ROM for many of the database fields. To find database entries which describe information published by author “Smith”, for example, you do not have to search through all fields of the database – which would be a time-consuming task – but you can tell EMBL-Search to use the “Author” field of the database exclusively. To find out how index files map to flat file line types consult the document “EMBL CD-ROM – Indices” supplied with your CD-ROM.
The fields that can be searched in the selected database are shown in the popup menus to the right of the text edit boxes in a query window.

A database query may consist of up to five subqueries. Each subquery is limited to a specific database field chosen from the popup menu. Database fields not available for the selected database are dimmed out from this menu.

The text edit boxes are used to enter the actual search strings. Text can be entered manually or copied from the index using the browser tool. See the Section “The Index Browser” below for more details about the index browser. Search strings are not case-sensitive, entering kinase, KINASE, or KiNaSe does not make any difference. The maximum length of a search string is 255 characters.

A search string is made up of individual search terms and Boolean operators. A search term can be a single word or a phrase, for instance “kinase”, “smith”, “thiol protease”, “immunoglobulin light chain”. If search terms are typed in which consist of multiple words, EMBL-Search will always try to exactly match the whole phrase.

Note: Some query languages imply a logical AND or OR if a multi-word phrase is entered. This is not true for EMBL-Search. “Protein kinase” is not the same as “protein OR kinase” or “protein  AND kinase”.

Search strings may contain the Boolean operators AND, OR, and NOT. These words are reserved and can not be used as search terms, that, is one can not look for these words in the database.

•    The AND operator
If search terms are connected by AND an entry must contain all terms to be recognised as a hit. The query “Smith and Jones” (when the database field “Author” is chosen) finds all database entries which contain both authors, “Smith” and “Jones”.

•    The OR operator
If search terms are connected by OR an entry is recognised as a hit if it contains at least one of them (or more). The query “Smith or Jones”  (when the database field “Author” is chosen) finds all database entries which contain the author “Smith” or the author “Jones” or both.

•    The NOT operator
A NOT in front of a search term tells EMBL-Search to ignore those entries which contain this term. The query “Smith and not Jones”  (when the database field “Author” is chosen) finds all database entries which contain the author “Smith” but do not contain the author “Jones”.

Search strings are simply evaluated from the left to the right. All operators have the same precedence.

Due to this fact, changing the order of search terms or operators may yield very different results!

For example, the queries “Smith and Jones or Miller” and “Jones or Miller and Smith” are not the same. If you query the database for “Smith and Jones or Miller” EMBL-Search will first look for all entries with author “Smith”, will then identify those which also contain the author “Jones” and throw away the rest, and will finally add to the result list those entries with the author “Miller”. The query therefore returns all entries which contain both authors “Smith” and “Jones” or contain the author “Miller” or all three of them. When it evaluates the query “Jones or Miller and Smith” instead, EMBL-Search will first find all entries with “Jones”, add all entries with “Miller”, and will finally go through this list and retain only those entries which contain “Smith”. The query thus returns all entries which contain either the author “Jones” or the author “Miller”, but additionally they must all contain the author “Smith”.

If you are not certain about the spelling of a word or a phrase, consult the index by using the index browser tool. You may also use the wild card character * at the end of a search term. EMBL-Search will then find all words which begin with the characters you typed in but may have different endings. For example, whereas “protein kinase” will only identify entries where the phrase “protein kinase” appears, “protein kinase*” will also find entries which contain the phrase “protein kinases”. “Kin*”, however, would not only find “kinase” and “kinases” but also other words such as “kinetics” or “kinky”.

Note: The wild card character is not valid at the beginning or in the middle of a search term.

Most common queries are simple and limited to one database field only. In these cases you would type in the search string into the first (or any other) text box of a query window, select the database field from the popup menu to its right, and click Search Database to start the search. More complicated questions which are not limited to only one database field require the use of subqueries.

For each subquery fill in one text edit box and select a database field from the popup menus. Do not leave blank boxes between subqueries. Subqueries are connected by global logical (Boolean) AND or OR operators which can be changed by using the buttons labelled “Connect by Boolean”.

Subqueries can also be used for more complicated queries within one database field, of course. For example, to find entries which contain sequences reported by Smith and Jones or by Miller and Webster, the simple query “Smith and Jones or Miller and Webster” would not work, because AND does not take precedence over OR. Instead, this query could be split into two subqueries “Smith and Jones” and “Miller and Webster”, both applied to the “Author” field and joined by Boolean OR.

Note: The maximum number of hits a query can return is 16,000. This is the total number after evaluating all subqueries. Single subqueries may yield more than 16,000 hits.

  The Index Browser

After clicking the Browse Index button in a query window, a dialog box will pop up. 
This dialog box displays the contents of the index you have selected from the query window’s database field popup menu in a convenient manner. It allows you to browse through the index and to copy search words to the query window easily.

The browser tool shows a list of words or phrases contained in the selected database field and the number of database entries in which those words occur. To locate a certain word quickly, for example to check its spelling, simply type in its first characters and click the Find button. The list then scrolls to the first word in the index starting with the characters you have entered. This lookup of words is case-insensitive; wild card characters are not permitted. You may then page through the list by using the scroll bar at the right or the arrow keys on your keyboard. The special keys on Apple’s extended keyboard are supported as well.

Words or phrases from the index can be copied to the query window by clicking in a line to select it and then clicking the Accept button. The browser window closes and the selected word or phrase is inserted at the current insertion point into the active text edit box of the query window. As a short-cut words can be copied by double-clicking. To leave the index browser without selecting words, click Cancel.

The number of individual items in the index is shown underneath the word list.

The Result Window

The result window lists all hits a database query returns in alphabetical order. For each hit the database entry name, its primary accession number, the sequence length, and a short description of the entry is presented.

The total number of hits is shown in the upper left corner. The number of hits that can be displayed is only limited by the maximum number of hits a query may return (16,000).
Individual hits can be selected by standard Macintosh clicking techniques. Single mouse clicks select individual entries. Holding down the Shift key allows continuous selection of multiple entries whereas the use of the Command (Cmd) key allows discontinuous selection of entries. EMBL-Search also supports drag-selection. If you hold down the Shift or Command key when you click in a description line and then move the mouse up or down without releasing the mouse button, all lines you move over will be selected. If you move the arrow pointer across the bottom or top of the window, the list will be scrolled up or down, respectively.

The number of selected entries is shown next to the number of total entries. A quick way to select or unselect all entries is to use the Select All and Select None commands from the Edit menu.

The Print command from the File menu allows you to get a printout of the results of a query. Result lists may be stored to disk by using the Save or Save As commands from the File menu and be further manipulated by other programs. They can be loaded back later with the Load Results command. Highlighted entry descriptions can also be copied to the Clipboard using Copy.

Note: EMBL-Search checks whether result files that it attempts to read in are compatible with the currently installed CD-ROM. See the description of result files in Chapter 7 ,“Files”, for restrictions.

  Exporting Database Entries

Selected database entries can be exported to disk by clicking the Export Selection button or choose Export Selection from the File menu. A dialog box will pop up:

The sequence format currently selected is shown at the bottom. Use the Sequence Format command from the Prefs menu to change it. If necessary, edit the filename provided by EMBL-Search and click Save to write the selected database entry to disk. If more than one entry is selected in the result window, the Save All button becomes active and allows you to write all entries into a single file. Use the Save button instead to store each entry separately; for each entry you will be asked for a new filename. You can use Save All at any time to write the remaining entries into a single file. Clicking the Skip button tells EMBL-Search to ignore the current entry and continue with the next one. The Cancel button stops the export process.

Note: It is not possible to write a set of database entries into a single file if Staden format is chosen. In this case, the Save All button will be dimmed.

While database entries are exported to disk, a dialog window is displayed which shows the name of the entry currently being saved. Extracting entries from the database can be a time-consuming task, especially if several hundreds of entries are processed. However, if you are using MultiFinder or System , you may switch to some other application program while the export progress window is visible and let the export proceed in the background.

The extraction of entries from the database can be interrupted at any time by clicking the Stop button or by typing Cmd-Period.

The Entry Display Window

This window is used to examine individual database entries. It is opened when the user double-clicks on an entry description line in a result window, or when the Cross-References command of the Others menu is used to quickly move between the EMBL and SWISS-PROT database. The window is an exact representation of entries in the original EMBL/SWISS-PROT format regardless of the format chosen from the Prefs menu. Entries of arbitrary size can be displayed in this window.

The entry display window is a normal Macintosh window which can be moved or resized. The Select All command from the Edit menu selects the complete contents of this window. The selection of parts of an entry is not supported at present. The contents of an entry display window can be printed using the Print menu command or saved to disk with the Save or Save As command. When an entry is saved, the sequence format chosen from the Prefs menu is used. Selected text can also be copied to the Clipboard using the Copy menu command.

  Cross-References

If a database entry contains DR lines which point to related entries in the EMBL or SWISS-PROT database, the Cross-References submenu of the Others menu becomes active and allows you to quickly move to the cross-referenced entries.

Menu Reference

This chapter describes each of the EMBL-Search menu commands. It is organised by menu, from left to right along the menu bar. Within each menu, commands are described in the order in which they appear in the menu.

  The Apple Menu

• About EMBL-Search...
This command tells you what version of EMBL-Search you are using. A mouse click or any keystroke ends the display.

• EMBL-Search Help...
This command activates the EMBL-Search help facility which offers an on-line version of this manual.

Under System , this command is additionally available under the Help menu.
The Help key on Apple’s extended keyboard is equivalent to the EMBL-Search Help command.

  The File Menu

• New (or Cmd-N)
This command opens a new, empty query window. The New command is not available if the maximum number of windows is already open.

• Open Query... (or Cmd-O)
This command displays a directory dialog box which lets you select an existing query file on the disk and open it for editing. This command is not available if the maximum number of windows is already open.

Note: Only files created by EMBL-Search will be visible in the dialog box.

• Load Results... (or Cmd-L)
This command allows you to pick an existing result file from a directory dialog box. Its content is presented in a new result window. This command is not available if the maximum number of windows is already open.

Note: Only files created by EMBL-Search will be visible in the dialog box.

• Close (or Cmd-W)
This command closes the active window and is the same as clicking in the active window’s close box. If the content of this window has been modified since it was last saved, a dialog box will ask you if you want to save the changes, discard them, or cancel the Close command. If the checkbox labelled “Confirm changes” in the “General Options” dialog box is not checked or if you hold down the Shift key when you close a window, changes are discarded silently. 

Note: To quickly close all windows simultaneously hold down the Options key while choosing Close or clicking into a window’s close box.

• Save (or Cmd-S)
This command saves the content of the active window to disk. If the window has not been saved yet, a dialog box will ask you to name the file. If the Save command is used when an entry display window is active, the database entry is stored in the format selected from the Sequence Format hierarchical menu.

• Save As...
This command lets you save the current window under another name. The original file remains unchanged. If the Save As command is used when an entry display window is active, the database entry is saved in the format selected from the Sequence Format hierarchical menu.

• Export Selection...
This command is only available if the active window is a result window. It is equivalent to clicking the Export Selection button in a result window. This command exports all entries selected in the active window to disk, using the sequence file format and file creator chosen from the Prefs menu.

• Page Setup
Presents the standard page setup dialog box which lets you select paper size, orientation and several printer-specific options. See your Macintosh owner’s manual for details.

• Print... (or Cmd-P)
This command lets you print the contents of the active window. The Print command is not available for query windows. Each page of the printout has a header with the window name and the page number and a footer showing the program name and the current date and time. To interrupt printing, press Cmd-Period or Escape.

• Quit (or Cmd-Q)
This command terminates EMBL-Search and gets you back to the Finder. If the “Confirm changes before closing a window” option from the “General Options” dialog box is on, then for each window whose content has changed since it was last saved EMBL-Search asks you to save or discard the changes or to interrupt the Quit command. Changes are discarded without prompting if the Shift key is held down when Quit is chosen.

  The Edit Menu

Note: Command-key equivalents of the Cut, Copy, Paste and Clear commands are available in dialog boxes and can be used to insert text in or move text around text edit fields within dialog boxes.

• Undo (or Cmd-Z)
This command is not implemented in the current version of EMBL-Search and therefore dimmed.

• Cut (or Cmd-X)
The Cut command removes selected text and places it in the Clipboard. It replaces the current contents of the Clipboard (if there are any). This command is only available in query windows or dialog boxes.

• Copy (or Cmd-C)
This command copies selected text and places it in the Clipboard. It replaces the current contents of the Clipboard (if there are any). This command can be used to transfer hits displayed in a result window or a database entry shown in a display window from EMBL-Search to other programs.

• Paste (or Cmd-V)
This command copies the contents of the Clipboard to the current insertion point of the active window. Any currently selected text is overwritten. Paste is not available if a result or entry display window is active.

• Clear
This command clears the selected text. The selection is not placed on the Clipboard. The Clear key on your keyboard is equivalent to the Clear command.

• Select All (or Cmd-A)
This command selects all text in the current result or entry display window.

• Select None
This command is the exact opposite of the Select All command. It unselects all text from the current result or entry display window.

• Duplicate Query (or Cmd-D)
This command opens a new query window which is an exact copy of the current one. This is useful if you want to investigate different versions of a query because it allows you to go back to the original question easily. This command is dimmed if the maximum number of windows is already open.

  The Others Menu

• Show Database Info (or Cmd-I)
This command displays a dialog box which contains the release number, the release date and the number of database entries of the EMBL and the SWISS-PROT databases.

• Cross-References
This is a hierarchical menu which is only available if an entry display window is active and the database entry shown in that window contains cross-references to other EMBL or SWISS-PROT database entries. Both databases use the DR line type to point to related entries in other databases. These links are utilised by EMBL-Search to build the Cross-References menu. It allows you to easily “jump” between the EMBL and SWISS-PROT databases.

For each DR line the hierarchical menu contains an item with the accession number and the entry name (in brackets) of the entry referred to. Choosing one of these items opens a new entry display window showing this entry. The All command opens new entry display windows for all cross-referenced entries simultaneously.

  The Prefs Menu

Several global preferences can be changed from within this menu. Their settings are stored in the file EMBL-Search Prefs in the System Folder (or Preferences Folder under System ). To make changes permanent use the Save Preferences command. Otherwise changes will be lost when EMBL-Search quits.

• Sequence Format
This hierarchical menu presents a list of several commonly used file formats which can be chosen for exporting and saving database entries. The currently selected one is indicated by a checkmark.

EMBL format is the genuine EMBL/SWISS-PROT flat file format and an exact representation of the information stored on the CD-ROM.

Staden format is the sequence only, without any annotation. If Staden format is chosen, it is not possible to save multiple entries in one file. Instead, EMBL-Search creates one file per database entry if several entries are exported to disk.

PIR/NBRF format is used by PIR’s NAQ/PSQ/XQS software and looks like this:
>P1;CATG_RAT
CATHEPSIN G (EC 3.4.21.20) (FRAGMENT).
IIGGREARPNSHPYMAFLLIQSPEGL
*

FASTA format is used by William Pearson’s FASTA or NCBI’s BLAST sequence similarity searching tools. It looks like this:
>CATG_RAT - CATHEPSIN G (EC 3.4.21.20) (FRAGMENT).
IIGGREARPNSHPYMAFLLIQSPEGL

• Sequence File Creator
The Macintosh Finder allows you to open documents easily by double-clicking their icons. Each file on a Macintosh disk is characterised by a “creator signature” which is invisible to the user but which allows the Finder to link documents to the application program that has created them. You can pick one of several popular word processors from the Sequence File Creator menu to set the creator signature of text files created by EMBL-Search, so that you can open and further manipulate them with standard Macintosh word processors.

Use the Other command if your favourite word processor is not on that list. A directory dialog box appears and allows you to select another program.

Changing the file creator affects the results and database entry files created by EMBL-Search, but not the query files. Query files can only be read by EMBL-Search itself.

• Locate Directories...
This command is used to override the default method EMBL-Search uses to find the index files it needs.

When EMBL-Search starts up it scans all drives attached to the Macintosh for a disk whose name begins with EMBL and tries to locate the required index files on that disk. Database queries can be speeded up by copying the database index files from the CD-ROM to a hard disk. Index files can not be moved individually. Instead, the whole folder containing the indices for the EMBL or SWISS-PROT database must be copied. See Chapter 8 for more details on moving index files.

The Locate Directories command is used to tell EMBL-Search about the locations of index files copied to a hard disk.

This dialog box displays the current location of the EMBL and SWISS-PROT index folders as pathnames. A pathname “•CD-ROM•” means EMBL-Search will use its default method to find this folder. Click Change to alter the location. A directory dialog will box pop up.

Only directories are visible in this dialog box. Move to the directory where you have installed the index files. Use the Select button to select the highlighted folder. Use Select This Directory to select the directory you are currently in and whose name is shown in the popup menu at the top of the scrollable list. The Use CD-ROM button restores the default behaviour of EMBL-Search, that is, it tells EMBL-Search to use the index files on the CD-ROM.

• General Options...
This command lets you set the following options:

- Confirm changes before closing a window
When a window is closed or the Quit command is chosen from the File menu, EMBL-Search checks whether the content of this window has changed since it was last saved. In this case, a dialog box will appear and ask you to save the changes, discard them or cancel the Close or Quit command. Turn this option off or hold down the Shift key when you close a window to circumvent this dialog. Changes are then discarded without confirmation.

Warning: Turning this option off is potentially dangerous because it may result in loss of data.

- Open application with empty query screen
Turn this option on if you want to see an empty query window when you start up EMBL-Search.

• Save Preferences
This command saves the current settings to a preferences file in the System Folder (or the Preferences Folder under System ). Every time you use EMBL-Search it will read this file and use the saved settings. The values stored include the sequence format, the sequence file creator, the locations of the index file directories, and the options set with the “General Options” dialog.

Note: To return to “factory” settings just delete the EMBL-Search Prefs file from your System or Preferences Folder.

  The Windows Menu

This menu can be used to switch between windows quickly. Opening a new window adds its name to the bottom of the Windows menu, closing a window removes its name from the list. The currently active window is indicated by a checkmark to the left of its name. The Windows menu is particularly useful if many windows are open and some are covered completely by others.

• Rotate (or Cmd-R)
This command moves the front window to the back and activates the next window. Repeated use of the Rotate command circles through all windows currently open.

  The Help Menu

If you’re running System , the Help menu contains a copy of the EMBL-Search Help command from the Apple menu. EMBL-Search specific Balloon Help™ is not available in the present version.

Limitations and Known Bugs

•    The maximum number of windows that can be open
      simultaneously is 20. Under low memory conditions
      this value might be less.
•    The maximum number of hits a query may return is
      16,000.
•    If two windows have the same name, the Windows
      menu does not work properly.