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<html>
<head>
<title>
PS_GG_ALIGN - Profile/Sequence Global Gap Alignment
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
PS_GG_ALIGN <br> Profile/Sequence Global Gap Alignment
</h1>
<hr>
<p>
<b>PS_GG_ALIGN</b>
is a FORTRAN90 library which
implements some of the string
alignment algorithms described in the reference <b>[Chao]</b>.
</p>
<p>
These
algorithms carry out the computation in <I>linear space</I>, and compute
not just the optimal alignment score, but also the corresponding optimal
alignment. The only alignments considered are global, that is, the
entirety of both strings are compared. Gaps in the alignment are
assigned an affine gap penalty.
</p>
<p>
It's important to be able to compute alignments using "linear space",
that is, just a few vectors whose length <b>N</b> is equal to that
of a typical string. A quadratic algorithm would require a two
dimensional array of total dimension <b>N*N</b>. Realistic alignment
problems can involve strings of <b>N</b>=100,000 elements or more,
so a quadratic algorithm would be expensive or impossible to use.
</p>
<p>
The optimal alignment score is computed without explicitly constructing
the corresponding alignment. So a major feature of the algorithms is
how to backtrack from the score to retrieve the alignment. It is a matter
of some difficulty to recover the matching, particularly if the best
score was calculated with a linear space algorithm, which discards a
great deal of intermediate information. However, the linear space
algorithm implemented here can also compute the optimal matching, based
on the idea of a recursive subdivision of the problem.
</p>
<p>
This set of algorithms does not actually match a pair of sequences,
but rather matches a sequence to a "profile". A profile is constructed
based on information from many sequences, and can be thought of as
a "generalized sequence", or a set of indices, where for each index
we specify the likelihood that each possible nucleic acid will occur.
These likelihoods can then be used to score the alignments we consider
with the new candidate sequence.
</p>
<p>
This set of routines assumes that an insertion or deletion of length
<b>K</b> is penalized using an "affine gap penalty formula" of the form:
<blockquote>
Penalty = Gap_Open + K * Gap_Extend
</blockquote>
This choice of penalty function has a major effect on the form
of the matching algorithms, particularly in the linear space case.
For the profile problems covered by these algorithms, the gap penalties
are further adjusted using profile-position percentages specified by
the user.
</p>
<p>
Routines that use quadratic space are included as well, so the algorithms
can be compared for storage, speed, and correctness.
</p>
<h3 align = "center">
Licensing:
</h3>
<p>
The computer code and data files described and made available on this web page
are distributed under
<a href = "../../txt/gnu_lgpl.txt">the GNU LGPL license.</a>
</p>
<h3 align = "center">
Related Data and Programs:
</h3>
<p>
<a href = "../../f_src/ps_lg_align/ps_lg_align.html">
PS_LG_ALIGN</a>,
a FORTRAN90 library which
implements a profile/sequence local alignment using an affine gap penalty.
</p>
<p>
<a href = "../../f_src/ps_qg_align/ps_qg_align.html">
PS_QG_ALIGN</a>,
a FORTRAN90 library which
implements a profile/sequence quasiglobal alignment using an affine gap penalty.
</p>
<p>
<a href = "../../f_src/ss_gd_align/ss_gd_align.html">
SS_GD_ALIGN</a>,
a FORTRAN90 library which
globally aligns two sequences using a distance matrix.
</p>
<p>
<a href = "../../f_src/ss_gg_align/ss_gg_align.html">
SS_GG_ALIGN</a>,
a FORTRAN90 library which
globally aligns two sequences using an affine gap penalty.
</p>
<p>
<a href = "../../f_src/ss_lg_align/ss_lg_align.html">
SS_LG_ALIGN</a>,
a FORTRAN90 library which
locally aligns two sequences using an affine gap penalty.
</p>
<p>
<a href = "../../f_src/ss_qg_align/ss_qg_align.html">
SS_QG_ALIGN</a>,
a FORTRAN90 library which
quasi-globally aligns two sequences using an affine gap penalty.
</p>
<h3 align = "center">
Reference:
</h3>
<p>
<ol>
<li>
Kun-Mao Chao, Ross Hardison, Webb Miller,<br>
Recent Developments in Linear-Space Alignment Methods: A Survey,<br>
Journal of Computational Biology, <br>
Volume 1, Number 4, 1994, pages 271-291.
</li>
<li>
Eugene Myers, Webb Miller,<br>
Optimal Alignments in Linear Space,<br>
CABIOS,<br>
Volume 4, number 1, 1988, pages 11-17.
</li>
<li>
Albert Nijenhuis, Herbert Wilf,<br>
Combinatorial Algorithms for Computers and Calculators,<br>
Second Edition,<br>
Academic Press, 1978,<br>
ISBN: 0-12-519260-6,<br>
LC: QA164.N54.
</li>
<li>
Michael Waterman,<br>
Introduction to Computational Biology,<br>
Chapman and Hall, 1995,<br>
ISBN: 0412993910,<br>
LC: QH438.4.M33.W38.
</li>
</ol>
</p>
<h3 align = "center">
Source Code:
</h3>
<p>
<ul>
<li>
<a href = "ps_gg_align.f90">ps_gg_align.f90</a>, the source code;
</li>
<li>
<a href = "ps_gg_align.sh">ps_gg_align.sh</a>,
commands to compile the source code;
</li>
</ul>
</p>
<h3 align = "center">
Examples and Tests:
</h3>
<p>
<ul>
<li>
<a href = "profile.txt">profile.txt</a>, a sample profile scoring
data file.
</li>
<li>
<a href = "ps_gg_align_prb.f90">ps_gg_align_prb.f90</a>, a sample
program to read a profile scoring data file.
</li>
<li>
<a href = "ps_gg_align_prb.sh">ps_gg_align_prb.sh</a>,
commands to compile, link and run the source code.
</li>
<li>
<a href = "ps_gg_align_prb.out">ps_gg_align_prb.out</a>, output
from running the sample program.
</li>
</ul>
</p>
<h3 align = "center">
List of routines:
</h3>
<p>
<ul>
<li>
<b>A_INDEX</b> sets up a reverse index for the amino acid codes.
</li>
<li>
<b>A_TO_I</b> returns the index of an alphabetic character.
</li>
<li>
<b>CH_CAP</b> capitalizes a single character.
</li>
<li>
<b>I_SWAP</b> switches two integer values.
</li>
<li>
<b>I_TO_A</b> returns the I-th alphabetic character.
</li>
<li>
<b>IVEC_REVERSE</b> reverses the elements of an integer vector.
</li>
<li>
<b>IVEC2_COMPARE</b> compares pairs of integers stored in two vectors.
</li>
<li>
<b>IVEC2_SORT_A</b> ascending sorts a vector of pairs of integers.
</li>
<li>
<b>PROFILE_SCORE_PRINT</b> prints profile scoring data.
</li>
<li>
<b>PROFILE_SCORE_READ</b> reads profile scoring data from a file.
</li>
<li>
<b>PROFILE_SCORE_READ2</b> returns a small amount of information from a profile.
</li>
<li>
<b>PS_GG_BPQ</b> determines a global gap backward alignment path in quadratic space.
</li>
<li>
<b>PS_GG_BSL</b> determines a global gap backward alignment score in linear space.
</li>
<li>
<b>PS_GG_BSQ</b> determines a global gap backward alignment score in quadratic space.
</li>
<li>
<b>PS_GG_FPQ</b> determines a global gap forward alignment path in quadratic space.
</li>
<li>
<b>PS_GG_FSL</b> determines a global gap forward alignment score in linear space.
</li>
<li>
<b>PS_GG_FSQ</b> determines a global gap forward alignment score in quadratic space.
</li>
<li>
<b>PS_GG_MATCH_PRINT</b> prints a global gap alignment.
</li>
<li>
<b>PS_GG_RPL</b> determines a global gap recursive alignment path in linear space.
</li>
<li>
<b>PS_GG_RPL_POP</b> pops the data describing a subproblem off of the stack.
</li>
<li>
<b>PS_GG_RPL_PUSH</b> pushes the data describing a subproblem onto the stack.
</li>
<li>
<b>RVEC2_SUM_IMAX</b> returns the index of the maximum sum of two real vectors.
</li>
<li>
<b>S_EQI</b> is a case insensitive comparison of two strings for equality.
</li>
<li>
<b>S_TO_CVEC</b> converts a string to a character vector.
</li>
<li>
<b>S_TO_I</b> reads an integer value from a string.
</li>
<li>
<b>SORT_HEAP_EXTERNAL</b> externally sorts a list of items into linear order.
</li>
<li>
<b>TIMESTAMP</b> prints the current YMDHMS date as a time stamp.
</li>
<li>
<b>WORD_LAST_READ</b> returns the last word from a string.
</li>
<li>
<b>WORD_NEXT_READ</b> "reads" words from a string, one at a time.
</li>
</ul>
</p>
<p>
You can go up one level to <a href = "../f_src.html">
the FORTRAN90 source codes</a>.
</p>
<hr>
<i>
Last revised on 17 December 2007.
</i>
<!-- John Burkardt -->
</body>
</html>