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