CSC

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.

• Load sequences ( see section Reading in sequences)
• Save ( see section Save)
• Change directory
• Sequence manager ( see section Sequence manager)
• Exit

Spin View Menu

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

• Results manager ( see section Result manager)
• Sequence display ( see section Sequence display)

Spin Options Menu

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

• Change protein score matrix ( see section Changing the score matrix)
• Set protein alignment symbols (see section Set protein alignment symbols)
• Configure maximum number of matches (see section Changing the maximum number of matches)
• Configure default number of matches ( see section Changing the default number of matches)
• Hide duplicate matches (see section Hide duplicate matches)
• Set fonts
• Colours

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).

• Horizontal (see section Change the active sequence)
• Vertical (see section Change the active sequence)
• Set range (see section Set the range)
• Copy (see section Copy sequence)
• Complement sequence (see section Complement sequence)
• Interconvert t and u (see section Interconvert t and u)
• Translate sequence (see section Translate sequence)
• Scramble sequence (see section Scramble sequence)
• Sequence type (see section Sequence type)
• Rotate sequence (see section Rotate sequence)
• Save (see section Save sequence)
• Delete (see section Delete sequence)

Spin Statistics Menu

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

• Count sequence composition ( see section Count Sequence Composition)
• Plot base composition ( see section Plot base composition)
• Count dinucleotide frequencies ( see section Count Dinucleotide Frequencies).

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.

• Set genetic code ( see section Set genetic code)
• Translate ( see section Translation - general),
• Find open reading frames ( see section Find open reading frames)
• Calculate and write codon table to disk (see section Calculate codon usage)

Spin Search Menu

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

• Protein genes: Codon pref ( see section Codon usage method)
• Protein genes: Author test ( see section Author test)
• Protein genes: Base bias ( see section Uneven positional base preferences)
• tRNA genes ( see section tRNA search)
• Search for string (DNA) ( see section Subsequence search)
• Restriction enzyme map ( see section Restriction enzyme search)
• Plot start codons ( see section Start codon search)
• Plot stop codons ( see section Stop codon search)
• Search for splice junctions ( see section Splice site search)
• Search using weight matrix ( see section Motif search)

Spin Comparison Menu

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

• Find similar spans ( see section Finding Similar Spans)
• Find matching words ( see section Finding Matching Words)
• Find best diagonals ( see section Finding the Best Diagonals)
• Align sequences ( see section Aligning Sequences Globally)
• Local alignment ( see section Aligning Sequences Locally)

Spin Emboss Menu

Spin provides a graphical user interface for most of the the programs contained in EMBOSS http://www.hgmp.mrc.ac.uk/Software/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.