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1.How does GDE for Linux works ?
2. Which bioinformatics programs can be accessed using the GDE for Linux interface ? And which programs need to be installed together with GDE for Linux ?
3. What I need to install GDE for Linux?
4. Installation Common Problems ?
5. Error messages, Troubleshooting.
6. GDE for Linux can be adapted for my research ?
7. How can I integrate specific sequence databases and datasets for sequence analysis ?
8. Automatic Integration using the PERL scripts.
9. Manually adding a DNA sequence database in XYLEM
10. Manually adding a DNA sequence database for local BLAST searches.
11. Manually adding a DNA or amino acid sequences aligments in the sequence database menu
12.Which organism had been integrated with GDE for Linux ? Microbial interface development.
1.How does GDE for Linux works ?
GDE main advantage is the ability to ?wrap? around a wide range
of bioinformatics programs and display the program output. GDE work as
a graphical interface between bioinformatics modules.
Although to access bioinformatics programs using GDE depend on:
1. Install the desired software (e.g. install clustalw for
multiple alignment, readseq for sequence conversion, and phylip for
phylogenetic
analysis).
2. Learn the desired bioinformatics software command line codes, and
the input/output formats.
3. Edit the GDE menu file control (.GDEmenus) and integrate the novel
bioinformatics software codes.
click
here for an example
2. Which bioinformatics programs can be
accessed using the GDE for Linux interface ? And which programs
need to be
installed together with GDE for Linux ?
Many bioinformatics software had already been integrated in the GDE
menu, menu code can be downloaded and easily integrated !! List of bioinformatics software integrated
with GDE
for Linux.
Also, learning to write code for software integration is not difficult.
This simply involves editing a unique file controlling the menu
appearance
(.GDE menus).
Some bioinformatics software for basic sequence manipulation
should be installed together with GDE for Linux executables. For basic
sequence
analysis we recommend installing the following programs: Readseq -
sequence
conversion, Clustalw - multiple alignment, BLAST - similarity
search,
Phylip - phylogenetic analysis, and Treetool - phylogenetic tree
manipulation.
The GDE for Linux distribution is already integrated with the listed
software.
3. What I need to install GDE for Linux?
Firstly you need a Linux system ! GDE for Linux had been
tested
in several GNU/Linux distributions and appear to work well.
You will need to download the program executables, Xview
libraries, and all the bioinformatics software that you want to use.
You can find the files at the download section
Installing GDE for Linux it is not a very difficult task, please follow the installation instructions.
4. Installation Common Problems ?
The main problems in GDE for Linux installation arise for not following
all the installation steps. Be sure that you had followed the
following items:
1. Install the XView libraries.
2. Install the basic bioinformatics software.
3. Install the GDE linux executables.
4. Setup the GDE_HELP_DIR environment variable.
5. Error messages, Troubleshooting.
Error: XView warning: Notified error: Unknown client
That is a warning message, please ignore, this do not cause any
problem.
GDE for Linux is not starting.
Error Message: .GDEmenus file not in the home, local, or
GDE_HELP_DIR directory
Normally this is caused when the system can not read the GDE_HELP_DIR
variable.
Fixing: setup the GDE_HELP_DIR variable.
bash:
[your_host] $ export GDE_HELP_DIR=/usr/local/biotools/GDE/CORE
tcsh:
[your_host] $ setenv GDE_HELP_DIR /usr/local/biotools/GDE/CORE
Error Message: segmentation fault
Normally this is caused when the GDE menu control file (.GDEmenus) had
been edited and contain errors.
Fixing: Correct the menu code that you edited, a tutorial for writing menu code is provided
.
Copy the previous GDE menu file to .GDEmenus, Please remember of making
.GDEmenus backups !
GDE for Linux started, but when trying to open a sequence file crash !
Error Message:UniqueID(): Failed to get host name.
GDE for Linux can not get your computer host name.
Fixing: Be sure that your host name and alias had been correct written
to /etc/hosts/
Alternatively: Setup the host name of your local computer (this will
not change your network configurations), with just the computer name
(without extensions and numbers)
[your_host] $ hostname
hostname.localnetwork
# Your hostname will be displayed.
[your_host] $ hostname ostname.localnetwork
[your_host] $ xhost +
[your_host] $ hostname hostname
[your_host] $ xhost +
6. GDE for Linux can be adapted for my
research ?
One of the things that I like more about the GDE interface, it is the
possibility to search local sequence databases, and to import specific
sequence alignments from the menu.
We work a lot with HIV evolutionary analysis, and we access locally the
complete HIV GenBank sequences, We design an HIV interface
for
local access that contains specific HIV Genbank , BLAST formatted
and
phylogenetic databases.
Also adding novel sequence databases and datasets for specific analysis
is easy and decrease a lot the the time sequence analysis, as it is
possible to run several sequence databases searches locally and it is
easy to import pre-analysed datasets.
7. How can I integrate specific sequence databases and datasets for sequence analysis ?
Integration of sequence database and datasets can be performed
in two ways: by manually editing the GDE menu file, and/or by using the
automated PERL scripts that we developed.
Basically you can integrate sequences databases to be :
Searched using the XYLEM project (similar Entrez-NCBI, but locally at
your server), homology search by BLAST, or to be important in the
GDE interface
8. Automatic Integration using the
PERL scripts.
Four PERL scripts are available together with the distribution
at the bin directory (usr/local/biotools/GDE/bin/)
Copy the PERL scripts from the bin directory in the
distribution (/usr/local/biotools/GDE/bin/)
* installBLASTDBDNA.pl - accessory script for automatic integrate
a new BLAST formatted database.
Copy the blast (/usr/local/biotools/GDE/installBLASTDBDNA.pl
, and usr/local/biotools/GDE/installBLASTDBPROT.pl ) PERL scripts
to home GDE/bin/ directory.
[your_host] $ cp
/usr/local/biotools/GDE/installBLASTDBDNA.pl
/your_home/GDE/bin/
[your_host] $ cp
/usr/local/biotools/GDE/installBLASTDBPROT.pl
/your_home/GDE/bin/
Edit the scripts (installBLASTDBDNA.pl and
installBLASTDBPROT.pl) and setup the correct user scripts and database
paths.
e.g. for user john: home = john (script path =
/home/john/GDE/bin), database path (/home/john/GDE/db).
Next step is to edit the GDE menu file (.GDEmenus) to provide
the path where the SCRIPTS are locate.
Locate in the menu where the scripts are located:
9. Manually adding a DNA sequence
database in XYLEM.
NOTE: Before adding databases to XYLEM, you will need to
install the package and have the set of programs running.
1. Firstly you need to have a file that contain a DNA sequence
database in Genbank format. (e.g. dbfile)
2. Copy the file to the /your_home/GDE/db/
3. Execute the splitdb program
[your_host] $ splitdb -g dbfile anofile seqfile indfile
4. Make sure you have the XYLEM menu in GDE for Linux !
5. You can search for sequences using the FINDKEY option and extract
some sequences to the GDE interface.
For more information on the use of XYLEM package please visit BIRCH web
page.
BIRCH is a resource for molecular biology, consisting of software and
databases. Most of the programs and databases of BIRCH have been
unified through the Genetic Data Environment (GDE).
10. Manually adding a DNA sequence
database for local BLAST searches.
NOTE: Before adding databases to BLAST you will
need
to install the package and have the set of programs running.
1. Firstly you need to have a file that contain a DNA sequence
database in FASTA format. (e.g. blastfile.fasta)
2. Copy the file to the /your_home/GDE/db/
3. Execute the formatdb program
[your_host] $ formatdb -i blastfile.fasta -p F -o T
Formatdb will create six new files (blastfile.nhr, blastfile..nhi,
blastfile.nsd, blastfile.nsi, blastfile.nsq, formatdb.log)
4. Test making a blast search.
[your_host] $ blastall -p blastn -i blastfile.fasta -d
blastfile.fasta
5. Edit the GDE menu control file (.GDEmenus) in your home
directory
[your_host] $ gedit (or any other text editor) ~/.GDEmenus
6. In the menu file search for the BLAST menu code (The menu codes are writing in a single file as they appear in the menu, beginning by the File menu option.)
################ BLAST - blastn menu #########################
item:blastn
itemmethod:...
7. To add the new database add a entry to the BLASTDBDNA variable, by adding a field argchoice:databasename:/database/location
arg:BLASTDBDNA
argtype:choice_list
arglabel:Which Database
argchoice:blastfile name:/your_home/GDE/db/blastfile.fasta
argchoice:...
8. Restart gde (GDE will read the menu file and
create the new entry, GDE just read the .GDEmenus once, at program
starting.)
The new BLAST format database (blastfile.fasta) will appear in the blastn
option on the DNA/RNA menu.
9. Import sequences and perform BLAST search against the new
database.
11. Manually adding a DNA or amino acid sequences aligments in the sequence database menu
1. Firstly you need to have a file that contain a DNA sequence
database in FASTA format. (e.g. alignment.fasta)
2. Copy the file to the /your_home/GDE/db/.
3. Edit the GDE menu control file (.GDEmenus) in your home
directory
[your_host] $ gedit (or any other text editor) ~/.GDEmenus
4. In the menu file search for the SEQUENCE DATABASE menu code (The menu codes are writting in a single file as they appear in the menu, beginning by the File menu option.)
################ SEQUENCE DATABASE menu #########################
item:sequence database
itemmethod:...
7. To add the new database add a entry to the SEQFILE variable, by adding a field argchoice:filename:/file/location
arg:SEQFILE
argtype:choice_list
arglabel:Alignments
argchoice:argchoice:alignment
1:/your_home/GDE/db/aligment.fasta
argchoice:...
12. Which organism had been
integrated with GDE for Linux ? Microbial interface development.