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UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Jemboss – a Graphical User Interface for the EMBOSS
suite of programs
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
EMBOSSCommand line based
Options not obvious – must be remembered
JembossPoint and Click interface
Portable interface – use with PCs, Mac OSX, UNIX
Options listed in program form
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
embl:m93650
seqret -sequence em:m93650 -sbegin1 0 -send1 0 -nofirstonly -auto
>HSPAX6AN M93650 Human paired box gene (PAX6) homologue, complete cds
cagaggtcaggcttcgctaatgggccagtgaggagcggtggaggcgaggccggcgccgca
cacacacattaacacacttgagccatcaccaatcagcataggaatctgagaattgctctc
Remote server
Local computer
Databases
EMBL
accession =m93650
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
EMBOSS applications
Job managerMode
Local file manager
Tool bar
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Local file manager
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
home directorypreferred directory
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
confirm directory path
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
new default directory
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
EMBOSS applications
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Select appropriate program from the category menus
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Selection from alphabetical list, using the “Go To” field
programs are highlighted based unambiguous letters
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
input possibilities
calculates nature of sequence and default settings
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Database entry in format database:entry
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
drag and drop the file into the sequence field
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
File (path) now specified
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
cut and paste a sequence from elsewhere
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Mode
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Interactive mode – Jemboss is suspended until program has been completed
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
results tab
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
input files tab
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
command line tab
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Saved file. All graphics files MUST be saved with a .png extension
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Job managerMode
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
job status job is processed in the background
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
job status
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Results can be saved in exactly the same manner as before.
Note: no command line tab
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Tool bar
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
select an application
input file and command line information is displayed
Notes on the experiment or analysis may be saved to the server along with the results
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Disable parameters by shading (selected) or removing them (deselected)
Auto-refresh. More often for slower connection, less often for a faster connection.
Alteration of default home directory path setting
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
The server settings and environment information should be the same
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
Default output for Jemboss is fasta format, so this may have to be altered
This third party software has also been incorporated into Jemboss
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
This is the beginnings of a project management system.
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
UK MRC Human Genome Mapping Project Resource Centre
http://www.hgmp.mrc.ac.uk
The version should always be reported if there are any problems with the program
brief user guide
Recommended