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How to upload sequences:
During a session you work on our server, as you probably know. Any sequence file on which you want to perform an analyses must either be stored in your own working directory on the server or must be an entry of one of the available databases on the server.In order to transfer files between your computer and your Working Directory on the server you have to upload them.
To upload data onto the server use one of the following alternatives:
- The Upload button in the bottom frame of the Main window opens a mask where
you can submit data from your local computer to our server. You can transfer files or
use the Copy and Paste Area to upload sequence data which you manually
enter or copy and paste from another window.
For detailed instructions look through the help cards of the
Upload page
Please be aware that whenever you type in or edit a sequence your file must have
a special format. Otherwise you cannot use it as an input sequence during your
sessions. Use, therefore, the option Translate to GCG Format .
See also File Formats - If you want to upload a great numer of data files you should use FTP
(File Transfer Protocol) in order to save time.
Open a FTP session from a command line interphase (e.g. DOS window ) and
enter the following line:
ftp [ the internet address of the GCG server ]. Example:
ftp genius.embnet.dkfz-heidelberg.de Press the Return key. You will usually see a lot of messages. Then you are asked to enter your user ID and password. When you are successfully logged in you will find yourself in your Home Directory on the server side. Use the appropriate FTP commands:pwd The path of your current working directory will be displayed
(To find out where you are)cd [path] directory-name To change the directory on the server side Example: cd /smith/projectxy/directoryA lcd [path] directory-name To change the directory on your local computer ls [path] directory-name To view the contents of a directory on the server side !ls [path] directory-name To view the contents of a directory on your local computer put [path] file-name To send a file from your local computer to the server mput [path] file-names (use *,?) To send multiple files from your local computer to the server Example: mput C:/temp/myfile*.seq get file-name To receive a file from your current directory on the server mget file-names To receive multiple files from your current directory on the server bye To quit the FTP session
How to start an Analysis Program:
There are many ways to start an application. To give you an overview:- Select one of the listed applications in the upper frame of the Main window. A second window will leap up. There you specify an input sequence, change parameters or leave them as they are and press the Run button.
- OR: Type the name of the program and select the file containing the input sequence(s) out of a file browser in the lower frame of the Main window. (To view your files and subdirectories click onto Without working List .) Then click the Start button. Again a second window will pop-up, asking you for options and parameters. Press the Run button to start the application.
- OR: Type the name of the program and specify the file containing the input sequence(s) in the respective input boxes of the Main window. Then click the Start button.
- OR: Start with assembling a set of sequences that you want to analyse. Out of this "Working List" you select the input sequence and then choose the application you want to run.
During a session you are working on our server, as you probably know. Therefore, all
input sequences must either be stored in files in your personal directory on the server
(in this case type in the file name, e.g.
and specify the sequence type (Nucl./Prot.), if asked for), or type in the full path, if the input sequence file is not stored in your current directory, e.g.
or the input sequence must be an entry in one of the available databases. In this case please type in the name of the database and accession number, e.g.
For detailed instructions look through the help cards of the Main Window.
See also How to upload Sequences and Batch Queues
All result files that are created during your sessions are listed in the Result window . See section How to manage your Result Files
How to set your Working Directory:
Your current Working Directory is displayed in the Main window. It is the "active" directory at the moment. If you create result files during your session they will be stored in the "active" directory.To change your current directory click onto the displayed directory name. Then enter the full path of the "wanted" directory. If you want to know the correct path of the directory press the File button in the Main window.
In order to create a new directory type in a non-existing directory.
Note: You work on a UNIX server. Therefore, start the full path with a "/" (= root directory), e.g.
A more elegant way is to define projects. Using the new feature User projects
you can assign a Working Directory for each project.
For detailed instruction see User project .
How to use Working Lists
If you often work with this analyses package you might get tired typing in the same sequence specification over and over again. Therefore, you might want to create a Working List of the sequences you frequently work with. Simply assemble personal sequence files, database sequence entries, and/or files that contain multiple sequences. The list will be stored in your current Working Directory. Whenever you open a session the list will appear in your Main window. It becomes easier for you to work with sequences. To start an analysis program mark the sequence file you want to use as input and select the program.
Remember that a name of a Working
List can be freely chosen, but must end with .list .For detailed instructions look through the help cards of the HOWTOs and the Sequence Selector .
You can, of course, create more than one of these Working Lists and organize them by projects. See also How to define Projects
How to work with Patterns (Data Files)
Some programs require a Data File containing enzyme recognition sites, primers, or other patterns for their analyses. For example, some of the mapping programs require an enzyme Data File to generate a restriction map. Each program has a default Data File, so for the time being you don't have to worry about these Data Files. However, sometimes it might be useful to edit the patterns listed in these files. Therefore, each of these programs offers you a Pattern Chooser button in the Application window. Here you can define your personal pattern list. Each program uses its own Data File so that the pattern selected in one application does not apply when you work with another program.
File Formats:
- Single Sequence Files
Much of the work you perform may involve single sequences, that you wish to analyse. A Single Sequence File has the following format:
Head (optional) Any number of lines of text describing the sequence.
Dividing Line A single line containing two periods (..).
Sequence Contains the sequence information.Whenever you upload a sequence file onto the GCG server or whenever you edit a sequence file using a non-GCG program make sure that the file has this format. (e.g. use the program reformat or enable the option Translate to GCG Format in the Upload window.)
Human hemoglobin, alpha chain, 23 Jan 1998
. .
"VLSPADKTNVKAAW...
KLRVDPVNFKLLSHA... Each line should not be
longer than 125 characters. - List Files
A List file is what its name implies: a file containing a list of sequence names. You can use list files with any program that accepts multiple sequences as input. List files are very helpful for working with groups of sequences whose names do not have characters in common (so you cannot use wildcards), or for specifying sequences from multiple locations (such as different databases and files in your personal directory).
Some programs produce output files that are list files. They may include additional information, such as Multiple Sequence Files . However, this extra information will not affect the list file's performance.This is an example of a list file for heat shock proteins (HSP70).
The list contains
- single sequences from your personal directory
- database specification
. ./smith/projectxy/my_hsp70.seq
gb_ov:xlhsp70 Begin:488 End:2428 Stans:+ Circ:F Wgt:1.00 !heat shock protein 70
gb_ov:chhksp Begin:392 End:2293 Stans:+ Circ:F Wgt:1.00 !J02579 Chicken 70 kd
gb_pl:M27825 Begin:591 End:2618 Stans:+ Circ:F Wgt:1.00 !B. lactucae (hsp70)
- Data Files
Many programs require nonsequence information (data files), which they use to analyse a sequence. For example, the program map requires two data files, enzyme.dat, which associates restriction enzyme names with their corresponding recognition sites; and translate.txt, which associates codons with their corresponding amino acids.
All programs that work with Data Files have a default Data File, so you don't have to worry about it. However, you may want to change a Data File (see also How to work with Patterns (Data Files) ). The new Data File will be stored in your Working Directory. If you keep the name of the default Data File and run a program, it automatically finds your personal Data File and uses it for the analysis.
How to clean up:
The amount of disk space which is regularly available for storing files on the GCG server is limited. Therefore, dear user, you should clean up your directories regularly!- The easiest way to delete files is the Delete files from disk button in the Result window. Simply mark the output files which you don't need anymore and press this button. You should also clean up the list of applications from time to time.
- If you want to reorganize your directory subsystem you should open the File Manager by clicking onto the Files button in the Main window. Remove, rename, or copy files, create or delete directories in a few mouse clicks.
Batch Queues:
Most programs run in a few seconds. However, some applications, such as FastA, take longer. Because of this, these applications will start in a Batch Queue modus by default. Applications in a Batch Queue do not start immediately after clicking Run, but as soon as the server has less work to do. You can, of course, change this option in the Application window. To remove a job from a queue use the Remove/Kill
button in the Result window.
How to fetch Data Files and Sequences
With the Fetch button in the bottom frame of the Main window you get access to database sequences and data files provided by our server. Simply type in a specification. Example:
embl:Z68620 (database entry)
or
globin.seq
(file name)
You can even use here the wild characters (*,?) (e.g.GenBank:humhb*) but remember that there is a size limit for fetched data.
Press the Fetch button and you get what you asked for. You can view the files and/or save them in your Working Directory on the server side. The help cards in the Fetch help page give you further instructions.
How to define Regularly Repeated Jobs
This feature can be quite interesting whenever your research project requires you to run a certain application more frequently. With the Alerts utility you can run such applications of special interest automatically.To create and define a new regularly repeated job load the Application window and change the mode from NOW to the frequency of repetition you wish (daily, weekly, or monthly). After you activated the Run button this job will not start immediately. Instead it will be added to the table of Regularly Repeated Jobs and the programm will start at the time point specified. You can check the results of this regular job at anytime. They will be shown in the Result window.
The Alerts button in the Main window shows you a list of the regular jobs currently defined. In this window you can also change their frequency of repetition and schedule, or remove a job, however, no new job can be created.
How to define Projects
Create projects to avoid mixing up all your result files. With the new feature User Projects you can assign a new working directory, a default working list, and other special properties for each project. Access to your data becomes easier, because it is now arranged in subdirectories. Moreover, you can assign project colors helping you to distinguish applications of different projects in the Result window.For detailed instruction see User project .
How to manage your Result Files
To monitor how your job is progressing open the Result window. When a program is complete, the name of the output file appears in this window. Note that the name is automatically generated. You can identify the result file of a particular program by its ID number.- Rename
You may find that renaming your result files sometimes simplifies the handling of a large number of result files. You can rename output files using the Rename button. - Remove
Use the button Delete files from disk to delete marked result files from both the List of output files and from your Working Directory. DonŽt mix this up with the Remove Entries from list button where you can only edit the List of output files - Save or Download
The easiest way to save your result files on your local computer is to click onto the name of the file in the Result window. A window will pop up where the result file is displayed. Use the Netscape toolbar where youŽll find Save As... in the File pull down menu.
Graphic output files : Click into the frame where your graphic output is displayed before you choose
Save As.... Otherwise the wrong file might be saved.
See the Setup window to find out which graphic format suits your needs. Most of the time the default GIF format will be fine. - Print
Use the Netscape toolbar where youŽll find Print... in the File pull down menu to print your result files on the printer connected to your local computer. Remember you have to first open the result file. Netscape will only print what is displayed on your screen. If several windows are open only the window that is currently active will be printed. Simply click into the frame to activate it.
Graphic output files : Click into the frame where your graphic output is displayed before you choose
Print .... Otherwise the wrong file might be printed.
See the Setup window to find out which graphic format suits your needs. Most of the time the default GIF format will be fine.