GCG/helix FAQ: Unix

What is a FAQ?

FAQ stands for Frequently Asked Questions. This is a list of questions that are asked by many users, so it was thought to be worth compiling the list for the use of everybody.

This particular FAQ is designed to help users of the GCG Sequence Analysis Package at NIH. It includes answers to the questions that are most commonly asked by GCG users of the helix systems.

What is GCG?

GCG, also known as the Wisconsin Package, stands for Genetics Computer Group. It is an integrated software package of routines to access, manipulate and analyze nucleotide and protein sequences. For example, you can use the GCG package to:

enter sequences from a digitizer or keyboard and edit them.
manage and assemble nucleotide sequence fragments in a sequencing project.
calculate and display restriction digests and simulate RNA fingerprints.
compare sequences
search nucleic acid or protein sequence databases for sequences similar to your query sequence or sequence pattern.
create, edit, display and analyze multiple sequence alignments
determine and display evolutionary phylogenies from multiple sequence alignments
recognize terminators, repeats, protein coding regions, and other consensus patterns
predict and display optimal and suboptimal RNA secondary structures
identify sequence motifs in protein sequences and make predictions about peptide isolation
translate nucleic acid sequences into protein sequences and backtranslate protein sequences into nucleic acids.
predict optimal primers for PCR reactions

If you are interested in using GCG, see Using GCG at NIH.

What is helix?

The helix systems consist of a cluster of mainframe and supercomputer applications, network and telecommunication facilities at the Division of Computer Research and Technology at NIH. Among other software, the helix systems maintain and support the GCG package and several large nucleotide and protein databases. See the helix web page for information about getting a helix account.

What is GCG-Lite?

GCG-Lite is a World Wide Web interface to the more popular utilities within the Genetics Computer Group (GCG) suite of sequence analysis programs. It currently includes

Sequence locator/lookup
DNA Analysis tools such as Map, Mapsort, Prime, Reverse, Translate.
Protein Analysis Tools such as Motifs, Isoelectric, Helicalwheel, MapPeptide, PepPlot, PlotStructure, BackTranslate.
Sequence Comparison Tools such as Gap, Bestfit, DotPlot/Compare.

There is online help for all these tools.

How do I edit my files on helix?

There are several editors available on the helix system, and which one you find convenient depends on your level of familiarity with Unix, your workstation/communications setup, and your needs.

Pico is a simple fullscreen text editor that works with most workstation/communications setups. To edit your file, type 'pico filename'. For more info on pico, type 'man pico' at the helix prompt. Pico is recommended for new users.
Vi is a text editor that is based on a line editor, and will probably work on any Unix system. The commands are not as simple as pico, however. To edit a file, type 'vi filename'. For more info type 'man vi' at the helix prompt.
Jot is a mouse-based text editor which has cut-and- paste, pull-down menus. It will work only on a workstation running xwindows software, and is tuned for SGI machines. To edit the file, type 'jot filename', and for more info 'man jot'.
Emacs is a free, powerful editor from the GNU project, which can handle mail, shells, compiling and more. It has an extensive manual which is available from TASC.

What shell should I use on helix?

The Unix operating system has several flavours of command interpreters which will affect the behaviour and appearance of your helix session. New users are set up with the 'T-shell' (tcsh) by default, which has useful features such as file name completion and command line editing. Other shells you could choose to use are ksh, sh, and csh. To change your default shell, send a ptr to the helix staff. For more information on any shell, type 'man shell_name' at the helix prompt.

I don't know any Unix!

Fear not. Even with just a rudimentary knowledge of Unix, you can successfully use the GCG package on helix for your research. Some elementary commands are described below, but it's worth having a good introductory Unix book for reference. DCRT's Technical Information Office has several Unix books, such as 'Learning the Unix Operating System' and 'A Student's Guide to Unix', which are free to NIH personnel. You can order them from your helix account by typing 'pubware' at the helix prompt and following the instructions, or directly from the TIO's web page.

Basic Unix commands:

For detailed information on any command, type 'man command-name' at the helix prompt.

cat prints the contents of a file on your terminal, and can be used to create files.

helix% cat filename

will spit the contents of 'filename' on your screen.

cat > filename.txt
type in some junk here or maybe paste in a sequence

will put the words 'type in some junk here or maybe paste in a sequence' into a file called filename.txt.

more will display the contents of a file on your screen, one screen at a time.

helix% more temp.seq
LOCUS       MUSIVJR       393 bp    mRNA            ROD       25-MAY-1995
DEFINITION  Mus musculus germline immunoglobulin light chain variable region
            and joining region mRNA, 5' end.
ACCESSION   L35316
[....etc....]

cp copies files.

helix% cp test.seq globin.seq

will copy the contents of test.seq to globin.seq. If you already have a file called globin.seq in your directory, it will be overwritten.

mv renames files.

helix% mv test.seq globin.seq

will rename the file test.seq to globin.seq. If a file called globin.seq already exists in your directory, it will be overwritten.

rm removes files.

helix% rm globin.seq

will remove (delete) the file globin.seq.

mkdir creates directories.

helix% mkdir globinproject

will create a subdirectory called globinproject in your current working directory.

cd changes your working directory.

helix% cd globinproject

will move you from your current directory to the globinproject directory, if that is a subdirectory.

helix% cd ..

will move you one directory level up.

ls lists the files in your current directory.

helix% ls 
acc                 mouse_heavy.list2   mouse_light.list2
mouse_heavy.list    mouse_light.list    temp.seq

logout logs you out of your helix session.

How do I cite the GCG package?

GCG suggests that published research which utilized the GCG software package should cite:

               Wisconsin Package Version 9.1, 
               Genetics Computer Group (GCG), 
                   Madison, Wisc.

This information appears in the GCG Banner that is displayed each time you initialize GCG on helix. When GCG is updated on the helix systems, the banner will change, so you should use the latest citation that appears in the banner.

VAX (VMS) to Unix issues

If you've been using GCG on a VMS operating system, your sequence files should work fine with GCG on helix. However there is one thing to watch out for. VMS files are normally called NAME.EXT;v where v is the version number. A semicolon is a special character in Unix, and Unix file names usually don't have version numbers. You can still use your files by:

typing a backslash (\) character before the semicolon when you use the filename. For example:
```
helix% more LPA223.SEQ\;1 
```
A better option: rename the file to something more Unix-compatible. For a single file, you can do this by typing:
```
helix% mv LPA223.SEQ\;1 LPA223.SEQ
or
helix% mv LPA223.SEQ\;1 LPA223.SEQ.1
```
If you are going to be renaming lots of files, you can use the fnunconvert program on helix, which will rename the files. To see how it works, you can try:
```
helix% fnunconvert -p .
```
which will describe the name changes, but not actually do them.