first previous next last contents

Spin Menus

The main window for spin contains File, View, Options, Sequences, Statistics, Translation, Search, Comparison and Emboss menus.

Spin File Menu

The File menu includes sequence reading, saving and management options.

Spin View Menu

The View menu contains options to give access to the Results Manager, and to the Sequence Display.

Spin Options Menu

The Options menu contains options for configuring spin and its functions.

Spin Sequences Menu

The Sequences menu contain options for manipulating the sequences currently loaded into spin. All these operations are also obtainable from a pop up menu in the sequence manager ( see section Sequence manager).

Spin Statistics Menu

The Statistics menu contains the spin functions for analysing and plotting the composition of sequences.

Spin Translation Menu

The "Translation" menu contains options to set the genetic code, translate to protein, find open reading frames and to calculate codon tables.

Spin Search Menu

The "Search" menu contains a variety of different searching and analysis techniques.

Spin Comparison Menu

The Comparison menu contains the spin analytical functions for comparing and aligning the sequences.

Spin Emboss Menu

Spin provides a graphical user interface for most of the the programs contained in EMBOSS

Those that are not provided are the ones that deal with multiple sequence alignments and the various rarely used tools such as the ones for database indexing. There are a lot of programs in EMBOSS so cascading menus are used. As far as the user is concerned the EMBOSS programs appear as though part of spin - all results are plotted in the same way as for equivalent spin functions, the sequences can be viewed in the sequence displays, and textual results appear in the Output Window.

An important feature of EMBOSS is that it provides access to the sequence libraries.

Notes on configuring EMBOSS for use via spin are included in the package's /doc directory. In summary these notes state the following: After installing EMBOSS the main task is to create the dialogues and menus for spin. This is entirely automatic. The create_emboss_files program attempts to find the location for your installed EMBOSS release. From this is iterates through all of the acd files and produces tcl/tk GUIs for each program. These are placed in the $STADENROOT/lib/spin_emboss/acdtcl directory. An Emboss menu is added to Spin, with the menu specification being in $STADENROOT/tables/emboss_menu.

first previous next last contents
This page is maintained by staden-package. Last generated on 22 October 2002.