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<head>
<title>
COM, COMPARE
</title>
</head>
<h1 align=center>
COM, COMPARE
</h1>
<hr size="3">
<font color=#880000>
<b>
NAME
<br>
</b>
</font>
COM, COMPARE - compare two sequences.
<br><br>
<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>
COM
<br>
COM minimal_score segment_width
<br>
COM OFF
<br>
COM COR serial1 serial2
<br>
COM ZOO zoom_factor
<br>
COMPARE
<br>
COMPARE minimal_score segment_width
<br>
COMPARE OFF
<br>
COMPARE CORNER serial1 serial2
<br>
COMPARE ZOOM zoom_factor
<br><br>
<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>
Compare two sequences. Garlic mantains two sequence buffers: the main
sequence buffer and the reference sequence buffer. After initializing both
buffers, the command COMPARE may be used to prepare the plot with comparison
of these two sequences. Matching residues will be marked by dots or squares,
depending on the zoom factor. Dots or squares which represent residue pairs
which match exactly will be colored yellow, while residues which are
different but have similar properties will be colored red. The reference
sequence will be assigned to the horizontal (x) axis, while another
(investigated) sequence will be assigned to the vertical (y) axis.
<br><br>
The plot will contain only residues which belong to the segments for which
the score of matching residues is equal to or larger than minimal score.
The minimal score (the number of matching pairs) and the width of the
segment used for comparison may be specified by the user. Hard-coded
defaults are SEGMENT_WIDTH and MINIMAL_SCORE, defined in defines.h file.
The values used in the original garlic package:
SEGMENT_width=5, MINIMAL_SCORE=5.
<br><br>
<font color=#880000>
<b>
SCORING
<br>
</b>
</font>
Two sequences are compared using fixed width segments. The matrix shown below
is used to identify matching residues. It was inspired by Dayhoff PAM250
matrix. However, while PAM250 matrix contains a range of values, both
positive and negative, the only values used in the substitution matrix below
are zero and one. One is used to identify matching residue pairs and zero
for pairs which do not match.
<br><br>
<img src="substmat.gif">
<br><br>
The scoring scheme used in garlic is much simpler than the elaborate schemes
used in advanced programs for sequence alignments. However, this scheme is
still quite useful and I believe that many users will like to play with
the various segment widths and scores.
<br><br>
<font color=#880000>
<b>
KEYWORDS AND PARAMETERS
<br>
</b>
</font>
All keywords and associated parameters are explained in the table below.
Note that the minimal score may not exceed the segment width.
<br><br>
<table border=2 cellspacing=2 cellpading=0>
<td align="center">
KEYWORD AND/OR
<br>
PARAMETERS
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
None
</td>
<td align="left">
Draw sequence comparison, using default segment
<br>
width and default minimal score.
</td>
<tr>
<td align="left">
OFF
</td>
<td align="left">
Return to the main drawing mode. The same may
<br>
be achieved by hiting the ESCAPE key.
</td>
<tr>
<td align="left">
minimal_score segment_width
</td>
<td align="left">
Draw sequence comparison, using the specified
<br>
segment width and the specified minimal score.
<br>
Both parameters should be positive.
</td>
<tr>
<td align="left">
CORNER ref_offset main_offset
</td>
<td align="left">
Draw sequence comparison, but skip some leading
<br>
residues. Skip (ref_offset - 1) residues of
<br>
the reference sequence and (main_offset - 1)
<br>
residues of the main sequence.
</td>
</table>
<br>
<font color=#880000>
<b>
MOUSE USAGE
<br>
</b>
</font>
The pointing device (mouse) may be used to find the residue serial numbers
and names for matching pairs and residues which follow after them. After a
chosen pair is reached with the pointer, the information about this pair
and residues which follow them will be available in the output window
(the bottom right corner). Color codes: yellow is used for residues which
are equal, magenta for acceptable substitutions and red for mismatching
residues.
<br><br>
<img src="../mouse/outcomp.gif">
<br><br>
<font color=#880000>
<b>
EXAMPLES
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
COMMAND
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
load 9PAP.pdb
<br>
sel het
<br>
sel com
<br>
seq from 1
<br>
seq copy
<br>
load 1HUC.pdb
<br>
sel a,b/*/*/*
<br>
seq from 2
<br>
compare 8 10
</td>
<td align="left">
Load the structure of papain, select all hetero atoms and
<br>
then select the complement of this selection. The purpose
<br>
of this trick is to exclude all hetero atoms from selection.
<br>
Extract the sequence and copy it to the reference buffer.
<br><br>
After that, load the structure of human cathepsin B, select
<br>
chains A and B (one molecules consists of two chains), extract
<br>
the sequence and compare it with the content of the reference
<br>
buffer. The minimal score is 8 and the segment width is 10.
</td>
<tr>
<td align="left">
load 9PAP.pdb
<br>
sel het
<br>
sel com
<br>
seq from 1
<br>
seq copy
<br>
seq load sample.fasta
<br>
compare 6 7
</td>
<td align="left">
Load the structure of papain and copy the sequence to the
<br>
reference buffer using the same method as in the previous
<br>
example. Read the second sequence from the specified FASTA
<br>
file (one letter codes). Compare two sequences, using the
<br>
specified minimal score and segment width (5/7).
<br>
This is the typical usage of sequence comparison: compare
<br>
a fresh sequence with the sequence of a solved structure.
</td>
<tr>
<td align="left">
com zoom 4
</td>
<td align="left">
Change zoom factor to 4.
</td>
<tr>
<td align="left">
com cor 100 100
</td>
<td align="left">
Skip the first hundred residues of both sequences.
</td>
</table>
<br>
<font color=#880000>
<b>
NOTES
<br>
</b>
</font>
(1) You don't need protein 3D structures to compare two sequences. The minimal
information required for protein comparison is the primary structure, i.e.
the protein sequence.
<br><br>
<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>
The command SEQ (SEQUENCE) is used to manipulate the content of the main
sequence buffer and of the reference sequence buffer. LOAD is used to load
the PDB file. SELECT, ADD and RESTRICT are used for selection.
<br><br>
<hr size="3">
</html>
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