Jemboss Sequence List
Keywords: java, biology, bioinformatics, EMBOSS, GUI, Jemboss, computational biology, sequence analysis, interface

# Sequence List

This window allows users to store their commonly used sequences. A sequence file can be dragged from the file managers into this window or a database entry (e.g. sw:pax6_human) can simply be typed into the table. The files then can be dragged and dropped back into the program sequence fields in the main Jemboss window when required.

An EMBOSS list file contains "references" to sequences, for example the file could look like:
`opsd_abyko.fasta
sw:opsd_xenla
sw:opsd_c*
@another_list`

Selecting 'List' in the Sequence List table will automatically prepend the filename with '@' (indicating to EMBOSS that this is a list file) when it is dragged into a application sequence field.

If the 'Default' column is selected then this sequence will automatically be the input sequence used when an EMBOSS application is chosen.

The sequence length can be calculated by selecting the sequence and clicking on 'Calculate sequence attributes' under the 'Tools' menu. The sequence start and end positions will then be displayed.

Saving the sequence list, between Jemboss sessions, is not done automatically. Go to the tools menu and select 'Save Sequence List' if this table is to be used in the next Jemboss session. This simply creates '.jembossSeqList' file in the user's home directory. This will then be loaded in (unless deleted from the file system) on the next Jemboss launch.

A sequence file can be opened by selecting the sequence in the table and opening it from the 'File' menu. Extra rows can be added to the table and sequences can be deleted from the 'Tools' menu.