Introduction

Spin is an interactive and graphical program for analysing and comparing sequences. It contains functions to search for restriction sites, consensus sequences/motifs and protein coding regions, can analyse the composition of the sequence and translate DNA to protein. It also contains functions for locating segments of similarity within and between sequences, and for finding global and local alignments between pairs of sequences. To help assess the statistical significance of comparisons the program can calculate tables of expected and observed score frequencies for each score level. Most analytical functions which operate on single sequences add their graphical results to a "SPIN Sequence Plot" that is associated with the sequence being analysed. (An exception is the restriction enzyme search which produces its own separate window.) Most functions which compare pairs of sequences add their results to a "SPIN Sequence Comparison Plot". The SPIN Sequence Plot and the SPIN Sequence Comparison Plot each have associated sequence display windows: the Sequence Display and the Sequence Comparison Display. These allow the text of the sequences to be viewed and use cursors to show the corresponding positions in the graphical displays. The graphical plots can be zoomed, and cursors or crosshairs can be used to locate the positions of the individual results. Plots can be superimposed.

Summary of the Spin Single Sequence Functions

Spin's main single sequence analytical functions are accessed via the Statistics, Translation and Search menus. The "Statistics" menu contains options to count and plot the base composition and also to count the dinucleotide frequencies.

The "Translation" menu contains options to set the genetic code, translate to protein, find open reading frames and write the results in either feature table format or as fasta format protein sequence files, and to calculate codon tables.

The "Search" menu contains a variety of different searching techniques. "Protein genes" has four methods for finding protein genes, (accessed as a subcomponent of the Codon Usage Method), and. There is also a method to search for tRNA genes. It is also possible to perform subsequence or string searches and restriction enzyme searches. There are searches for start and stop codons, splice junction searches, and general motif searches using weight matrices.

Summary of the Spin Comparison Functions

This section outlines the functions obtained from the Comparison menu. All produce graphical and textual output. Using a score matrix, the "Find similar spans" function compares every segment of one sequence with all those of the other and reports those that reach a user defined score. The segments are of a fixed length (span) set by the user. To look for short matching segments of any length, and allowing gaps, a local dynamic programming routine can be used. The fastest routine for locating segments of similarity (and generally only suitable for DNA sequences) finds all identical subsequences (or words). For a quick global comparison of sequences using a combination of the Matching Words and Matching Spans algorithms the "Find best diagonals" algorithm can be used. Global alignments can be produced and plotted using a dynamic programming algorithm.

Introduction to the Spin User Interface

• The SPIN Sequence Plot
• The SPIN Sequence Display
• The SPIN Sequence Comparison Plot
• The SPIN Sequence Comparison Display

Spin has several main displays. The first is a top level window from which all the main options are selected and which receives textual results. Most analytical functions which operate on single sequences add their graphical results to a "SPIN Sequence Plot" that is associated with the sequence being analysed. (An exception is the restriction enzyme search which produces its own separate window.) Most functions which compare pairs of sequences add their results to a "SPIN Sequence Comparison Plot". The SPIN Sequence Plot and the SPIN Sequence Comparison Plot each have associated sequence display windows: the Sequence Display and the Sequence Comparison Display. These allow the text of the sequences to be viewed and use cursors to show the corresponding positions in the graphical displays.

Spin is best operated using a three button mouse, but alternative keybindings are available. Full details of the user interface are described elsewhere, and here we give an introduction based around a series of screenshots.

The main window (shown below) contains an Output Window for textual results, an Error window for error messages, and a series of menus arranged along the top. The contents of the two text windows can be searched, edited and saved. Each set of results is preceded by a header containing the time and date when it was generated.

As can be seen the main menu bar contains File, View, Options, Sequences, Statistics, Translation, Comparison, Search and Emboss menus. In general most functions add their graphical results to a "SPIN Sequence Plot", but those obtained from the Comparison menu add their results to a "SPIN Sequence Comparison Plot".

Introduction to the Spin Plot

Most of the spin functions display their results in a two-dimensional plot called a "spin plot". Sets of matches from a single invocation of a function are termed "a result". Each result is plotted using a single colour which can be configured via the results manager.

The figure shown below shows a spin plot window containing the results of a gene search method based on codon usage, superimposed on a search for stop codons. Each plot window contains a cross hair. Its x position is shown in sequence base numbers in the left hand box above the plot, and the y coordinate, expressed using the score values of the gene search, is shown in the right hand box.

At the right hand side of each panel is a set of square boxes with the same colours as the lines drawn in the adjacent plot. These icon-like objects represent individual results and allow the user to operate on them. For example at the right of the middle panel is a pop-up menu containing the items: "Information", "List results", "Configure", "Hide" and "Remove"..

These icons can also be used to drag and drop the results to which they correspond. This is activated by pressing the middle mouse button, or Alt left mouse button, over the box and then moving the cursor over the spin plot to the new location or anywhere outside the spin plot

Each spin plot window also contains a cursor that denotes the position of the cursor in the Sequence display window. The user can move a cursor by clicking and dragging with the middle mouse button, or Alt left mouse button. This will move the cursor in the sequence display and all other cursors displayed that relate to the sequence.

The graphical results can be zoomed and scrolled in both x and y directions. Zooming is achieved using the X and Y scale bars at the top left hand corner of the plot. The individual plots can be scrolled in y using the scroll bars attached to their right hand edge. The sequence can be scrolled using the scroll bar at the base of the plot.

To illustrate further uses of the program we include some more screen dumps below.

The figure above shows the results of a search for restriction enzymes.

The figure above is a plot of the base composition of a sequence.

The figure above shows the way in which the results of weight matrix searches for motifs are plotted.

The figure about shows the way in which the results of searches for splice junctions are plotted. The donor and acceptor predictions are separated and a different colour is used for each reading frame.

The figure above shows a method for finding protein coding regions which does not distinguish reading frame or strand.

The figure above shows how results from the tRNA gene search function are displayed in the Output window.

Introduction to the Spin Sequence Display

Spin also has a sequence display window in which the user can view the sequence in textual form. This window allows the user to scroll along the sequence. Users can view one or both strands, can switch on displays of the encoded amino acids in up to six reading frames, can switch on a display of the restriction enzyme sites, and can perform other simple subsequence or string searches to locate features in the sequence. In the figure shown below the user has switched on a three phase translation on the top strand, double stranded sequence, and a restriction enzyme search.

The sequence cursor can be under the control of the graphics cursor i.e. the cursor in the sequence viewer can be moved by the user dragging the cursor in the graphics window. Similarly the cursor in the graphics plots can be moved by the sequence viewer cursor.

Introduction to the Spin Sequence Comparison Plot

All of the spin comparison functions display their results as points or lines in a two-dimensional plot called a "Spin Sequence Comparison Plot". Sets of matches from a single invocation of a comparison command are termed "a result". Each result is plotted using a single colour which can be configured via the results manager.

The diagram above shows the results of a "Find similar spans" search (olive), and a "Find matching words" (red).

At the right hand side is a set of square boxes with the same colours as the dots drawn in the adjacent plot. These icon-like objects represent individual results and allow the user to operate on them. For example clicking with the right mouse button brings up the pop-up menu beneath the "matching words" result contains the results menu for this result. These icons can also be used to drag and drop the results to which they correspond. This is activated by pressing the middle mouse button, or Alt left mouse button, over the box and then moving the cursor over the Spin Sequence Comparison Plot to the new location or anywhere outside the Spin Sequence Comparison Plot.

Crosshairs can be turned on or off using the check button labelled "crosshairs". The x and y positions of the crosshairs are indicated in the two boxes to the right of the check box.

Each sequence displayed in a Spin Sequence Comparison Plot will have a cursor of a particular colour. In the picture above, the sequence on the horizontal axis has a vertical blue cursor whereas the sequence on the vertical axis has a horizontal olive green cursor. In general, the same sequence displayed in several Spin Sequence Comparison Plots will have a cursor of the same colour. The user can move a cursor by clicking and dragging with the middle mouse button, or with Alt left mouse button. This will move all other cursors displayed that relate to the sequence, whether they are in different Spin Sequence Comparison Plots or within the sequence display.

Plots can be enlarged either by resizing the window or zooming. Zooming is achieved by holding down the control key and right mouse button and dragging out a rectangle. This process can be repeated. The Back button will restore the plot to the previous magnification.

To illustrate further uses of the program we include some more screen dumps below.

The picture above shows the results after performing a "Find similar spans" comparison between the three reading frames of two DNA sequences, producing nine superimposed sets of results.

Local alignment searches join similar segments with lines. The above screen dump shows such an analysis in which genomic DNA containing 7 exons and is compared to its corresponding cDNA.

The above screendump shows a global alignment of the same pair of sequences.

Introduction to the Spin Sequence Comparison Display

A sequence comparison display is associated with a single set of results and can be invoked by bringing up a pop up menu for the required result, either from the Results manager, the Results menu in the Spin Sequence Comparison Plot, or the coloured square icon on the right of the plot.

The horizontal sequence is drawn above the vertical sequence and the central panel indicates characters which are identical. The buttons (< >) and (<< >>) scroll the sequences. Pressing the Lock button forces the sequences to scroll together. Movement of the sequences is also controlled by the scrollbars or by moving the corresponding cursor in the Spin Sequence Comparison Plot. The black cursors in the sequence display correspond to the position of the cursor in the Spin Sequence Comparison Plot. The sequences can be made to 'jump' to the nearest match in those results by pressing the "Nearest match" or "Nearest dot" buttons.