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Laurence H. Baker Center for Bioinformatics and Biological Statistics

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Sequence Analysis Servers

Online Analysis Tools
SeWeR

Microarray Database

Before asking any questions, please read this document.

How to use GCG?

GCG is installed on deepc2.psi.iastate.edu. To access it, you will need a user account on deepc2. Please contact xfzhao@iastate.edu for an account on deepc2.You can access directly by logging on deepc2 or by using the web interface.

There are three ways to run GCG: using the web interface for GCG provided by W2H, using the graphic user interface for GCG, SeqLab, and using the pure text-based command line.

Command line:

To run GCG from command line, you need to do the following:

1. Log on to deepc2 using ssh. Example: ssh deepc2.zool.iastate.edu -l username. Replace username by your lab's username on deepc2. You will be prompted for the password, enter your lab's password.

2. Enter the following commands:

  • csh
  • source /database/users/gcg/gcgstartup
  • gcg

You should have already initialized GCG then. From then on, you can run a GCG application by simply entering the name and hit "Return" (or "Enter"). For help, enter "genhelp".

SeqLab:

Using the graphic user interface for GCG, SeqLab, is recommended by the instructor of our recent GCG workshop, Mr. Steve Thompson. It is especially nice if you need to work with multiple sequence alignments. To run SeqLab, enter: (these are instructions on how to run it from a UNIX machine remotely, we will add the instructions on using PCs and Macs.)

1. Log on to deepc2 using the command: ssh -X deepc2.psi.iastate.edu -l your_lab's_username_on_deepc2

You will be prompted for your lab's password on deepc2. Enter it and you should have logged onto deepc2 then.

2. Enter the following commands:

  • csh
  • source /database/users/gcg/gcgstartup
  • gcg
  • seqlab &

The "&" is optional. It makes seqlab running in background and leaves the terminal active and can accept other commands. So, in a sense, you can run GCG from command line and using SeqLab at the same time with the same terminal.

Web Interface:

The web interface for GCG is currently set up using W2H. There may still be some problems in configuration to make it fully functional. Please let Xuefeng Zhao (xfzhao@iastate.edu) know if you find any problem. The web interface for GCG can be accessed at http://deepc2.psi.iastate.edu/w2h. From it, you can access your home directory on deepc2 on the web, run programs and manage the files. The installation of SeqWeb, the default web interface for GCG, requires significant changes to the web server. There are other programs other than GCG on that machine and they maybe affected by the changes to the web server. Hence, we will silently working on it to find a way to make SeqWeb work along with other programs' web interfaces. We will let you know about it once we are able to do it. For now, please use the W2H interface.

How to use EMBOSS?

EMBOSS (European Molecular Biology Open Software Suite) is a nice and free suite of sequence analysis programs. It is installed on deepc2 as well. It is recommended that you use them by the web interface which can be accessed at http://deepc2.psi.iastate.edu/w2h-emboss. Again, it sees your home directory on deepc2 and allows you to upload files from your local machines into it.

List of Microarray software available:

ImaGene

ImaGene is an automatic image analysis software from BioDiscovery. For more information, go to http://www.biodiscovery.com/imagene.asp. A copy of ImaGene was installed on a Windows machine in the Bioinformatics Facility at Bessey.

GeneSpring

We have recently purchased the new license for GeneSpring, and we installed it in the Bioinformatics Facility at Bessey Hall. For more information about GeneSpring, please visit its official site: http://www.sigenetics.com/cgi/SiG.cgi/Products/GeneSpring/index.smf

GeneTraffic

An ISU microarray database is set up with the GeneTraffic Multi database software on a dedicated server. The GeneTraffic microarray database can be accessed at http://microarray.plp.iastate.edu. The database can only be accessed by the ISU researchers. To request an account, please send an E-Mail to Dr. Xuefeng Zhao with the following information included:

  • Preferred Username (no space)
  • First Name
  • Last Name
  • Preferred Password
  • E-Mail Address
  • Telephone Number
  • Research Group
  • Department
  • Address

How to run phred/phrap/consed?

We have also installed the phred/phrap/consed package on deepc2. Unfortunately, there are no web interfaces for these program. We might work on it in the future to integrate them into either the GCG package or the EMBOSS package. The nice thing about the current setup, though, is that you can run phred on the sequencing trace files and the output FASTA files along with the original files are stored in your home directory on deepc2, you can then view or run GCG and EMBOSS programs using them as input over the web.

E-mail: lhb.bioinformatics@iastate.edu
URL: http://www.bioinformatics.iastate.edu/

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