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<html>
<head>
<title>
SS_GG_ALIGN - Sequence/sequence Global Gap Alignment
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
SS_GG_ALIGN <br> Sequence/sequence Global Gap Alignment
</h1>
<hr>
<p>
<b>SS_GG_ALIGN</b>
is a FORTRAN90 library which
implements some of the string
matching 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.
</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 "matching" being considered does not actually require that every
element of string <b>A</b> match an identical element of string <b>B</b>.
Instead, the matching algorithm is essentially looking for the cheapest
way of transforming one string into the other, allowing the operations of
"mutation" (change one letter to another), "deletion" (drop a string
of consecutive letters) and "insertion (insert a string of consecutive
letters). Thus, at the same time, we are measuring a sort of
evolutionary distance between two strings and a formal "editing
distance" between them.
</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.
(Compare the simpler "global distance" routines in
<a href = "../ss_gd_align/ss_gd_align.html">SS_GD_ALIGN</a>.)
</p>
<p>
The score for the actual best matching is determined without explicitly
constructing the best matching. It is a matter of some
difficulty to recover the matching corresponding to the best score.
This is particularly true if the algorithm is a linear space one, which
discards a great deal of intermediate information. However, it is
possible to set up a recursive algorithm which determines the best
alignment, using only linear space.
</p>
<p>
Routines that use quadratic space are included as well, so the algorithms
can be compared for storage, speed, and correctness.
</p>
<p>
The names of the scoring and path routines include information
about whether they use a forward, backward, or recursive algorithm,
whether they compute the score or the path, and whether they use
linear or quadratic space. Thus, the routine
<b>SS_GG_FSQ</b> uses the forward algorithm to compute the score,
with quadratic space requirements.
</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_gg_align/ps_gg_align.html">
PS_GG_ALIGN</a>,
a FORTRAN90 library which
implements a profile/sequence global alignment using an affine gap penalty.
</p>
<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_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>
Carl Branden, John Tooze,<br>
Introduction to Protein Structure,<br>
Second Edition,<br>
Garland Publishing, 1999,<br>
ISBN: 0815323050,<br>
LC: QP551.B7635.
</li>
<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>
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 = "ss_gg_align.f90">ss_gg_align.f90</a>, the source code;
</li>
<li>
<a href = "ss_gg_align.sh">ss_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 = "ss_gg_align_prb.f90">ss_gg_align_prb.f90</a>, test
routines;
</li>
<li>
<a href = "ss_gg_align_prb.sh">ss_gg_align_prb.sh</a>,
commands to compile, link and run the test routines;
</li>
<li>
<a href = "ss_gg_align_prb.out">ss_gg_align_prb.out</a>, the test
output.
</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_I4</b> returns the index of an alphabetic character.
</li>
<li>
<b>CH_CAP</b> capitalizes a single character.
</li>
<li>
<b>CHVEC2_PRINT</b> prints two vectors of characters.
</li>
<li>
<b>CHVEC_PRINT</b> prints a vector of characters.
</li>
<li>
<b>GET_SEED</b> returns a seed for the random number generator.
</li>
<li>
<b>I4_RANDOM</b> returns a random integer in a given range.
</li>
<li>
<b>I4_SWAP</b> switches two integer values.
</li>
<li>
<b>I4_TO_A</b> returns the I-th alphabetic character.
</li>
<li>
<b>I4_TO_AMINO_CODE</b> converts an integer to an amino code.
</li>
<li>
<b>I4VEC2_COMPARE</b> compares pairs of integers stored in two vectors.
</li>
<li>
<b>I4VEC2_PRINT</b> prints a pair of integer vectors, with an optional title.
</li>
<li>
<b>I4VEC2_SORT_A</b> ascending sorts a vector of pairs of integers.
</li>
<li>
<b>I4VEC_REVERSE</b> reverses the elements of an integer vector.
</li>
<li>
<b>MUTATE</b> applies a few mutations to a sequence.
</li>
<li>
<b>PAM120</b> returns the PAM 120 substitution matrix.
</li>
<li>
<b>PAM120_SCORE</b> computes a single entry sequence/sequence matching score.
</li>
<li>
<b>PAM200</b> returns the PAM 200 substitution matrix.
</li>
<li>
<b>PAM200_SCORE</b> computes a single entry sequence/sequence matching score.
</li>
<li>
<b>R4VEC2_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_I4</b> reads an integer value from a string.
</li>
<li>
<b>SIMPLE_SCORE</b> computes a single entry sequence/sequence matching score.
</li>
<li>
<b>SORT_HEAP_EXTERNAL</b> externally sorts a list of items into linear order.
</li>
<li>
<b>SS_GG_BPQ</b> determines a global gap backward alignment path in quadratic space.
</li>
<li>
<b>SS_GG_BSL</b> determines a global gap backward alignment score in linear space.
</li>
<li>
<b>SS_GG_BSQ</b> determines a global gap backward alignment score in quadratic space.
</li>
<li>
<b>SS_GG_FPQ</b> determines a global gap forward alignment path in quadratic space.
</li>
<li>
<b>SS_GG_FSL</b> determines a global gap forward alignment score in linear space.
</li>
<li>
<b>SS_GG_FSQ</b> determines a global gap forward alignment score in quadratic space.
</li>
<li>
<b>SS_GG_MATCH_PRINT</b> prints a global gap alignment.
</li>
<li>
<b>SS_GG_MATCH_SCORE</b> scores a global gap alignment.
</li>
<li>
<b>SS_GG_RPL</b> determines a global gap recursive alignment path in linear space.
</li>
<li>
<b>SS_GG_RPL_POP</b> pops the data describing a subproblem off of the stack.
</li>
<li>
<b>SS_GG_RPL_PUSH</b> pushes the data describing a subproblem onto the stack.
</li>
<li>
<b>TIMESTAMP</b> prints the current YMDHMS date as a time stamp.
</li>
<li>
<b>UNIFORM_01_SAMPLE</b> is a portable random number generator.
</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 28 December 2007.
</i>
<!-- John Burkardt -->
</body>
</html>