Sip is a program for comparing and aligning pairs of nucleic acid or protein sequences. The program, which is based around "dot matrix" plots, includes several methods of finding matches between pairs of sequences and ways of displaying them. The methods vary in speed and sensitivity. The two dimensional plots created by the comparison methods can be zoomed and crosshairs used to locate the positions of individual matches. The alignments between segments of the sequences can be examined using a display that enables the sequences to be slid passed one another. The sliding can be linked to the position of the crosshairs or the sequences can be positioned automatically to show the alignment of the nearest match.
To help assess the statistical significance of comparisons the program can calculate tables of expected and observed score frequencies for each score level ( see section Probabilities and expected numbers of matches). A dynamic programming algorithm for finding optimal alignments is included. DNA sequences can be complemented and translated so that they can be compared at the protein level.
The main window of SIP has the menus: "File", "View", "Options",
"Comparison" and "Help" at the top of the window.
The "File" menu contains the commands to extract sequences from either a
sequence library or a personal file (
see section Reading in sequences).
The "View" menu contains options to use the Sequence manager
(
see section Sequence manager), or the Results manager
(
see section Result manager).
The "Options" menu allows the user to change the score matrices for DNA or
protein sequences (
see section Changing the score matrix), change the maximum number of matches and the default
number of matches that are plotted (
see section Changing the maximum number of matches).
The "Comparison" menu contains the sequence comparison functions, including
"Find similar spans" (
see section Find similar spans), "Find matching words" (
see section Find matching words), "Find best
diagonals (
see section Find best diagonals), and "Align sequences", (
see section Align sequences). The first three
of these functions display their results as points or lines in a
two-dimensional plot called a "sip plot" (
see section Sip plot).
The picture below shows the results after preforming a "Find similar spans"
comparison between the three reading frames of two DNA sequences, producing
nine plots in all.
Beneath these are two text windows, the "Output window" which displays
any text output from the program and the "Error window" which displays
all error messages.
![[picture]](sip_top.gif.html)
(Click for full size image)
![[picture]](sip_plot.gif)
This page is maintained by
James Bonfield.
Last generated on 29 April 1996.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/sip_1.html