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<html>
<head>
<title>
SS_QG_ALIGN - Sequence/sequence Quasiglobal Gap Alignment
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
SS_QG_ALIGN <br> Sequence/sequence Quasiglobal Gap Alignment
</h1>
<hr>
<p>
<b>SS_QG_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>
The <i>quasiglobal</i> matching considered here is similar to the
global matching scheme, except that no penalty is applied for the
very first gap (a deletion or insertion, but not both), and the very
last one. This simple alteration in the global alignment scheme
facilitates the search for repeated patterns.
</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_QG_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_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>
<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, volume 4, number 1, 1988, pages 11-17.
</li>
<li>
Michael Waterman, <br>
Introduction to Computational Biology,<br>
Chapman and Hall, 1995.
</li>
</ol>
</p>
<h3 align = "center">
Source Code:
</h3>
<p>
<ul>
<li>
<a href = "ss_qg_align.f90">ss_qg_align.f90</a>, the source code;
</li>
<li>
<a href = "ss_qg_align.sh">ss_qg_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_qg_align_prb.f90">ss_qg_align_prb.f90</a>, test
routines;
</li>
<li>
<a href = "ss_qg_align_prb.sh">ss_qg_align_prb.sh</a>,
commands to compile,link and run the test routines;
</li>
<li>
<a href = "ss_qg_align_prb_output.txt">ss_qg_align_prb_output.txt</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_CHVEC</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_BSL</b> determines a global gap backward alignment score in linear space.
</li>
<li>
<b>SS_GG_FSL</b> determines a global gap forward alignment score in linear space.
</li>
<li>
<b>SS_QG_BOQ</b> determines the backward endpoint of a quasiglobal optimal local alignment.
</li>
<li>
<b>SS_QG_BPQ</b> determines a quasiglobal gap backward alignment path in quadratic space.
</li>
<li>
<b>SS_QG_BSL</b> determines a quasiglobal gap backward alignment score in linear space.
</li>
<li>
<b>SS_QG_BSQ</b> determines a quasiglobal gap backward alignment score in quadratic space.
</li>
<li>
<b>SS_QG_FOQ</b> determines the forward endpoint of a quasiglobal optimal local alignment.
</li>
<li>
<b>SS_QG_FPQ</b> determines a quasiglobal gap forward alignment path in quadratic space.
</li>
<li>
<b>SS_QG_FSL</b> determines a quasiglobal gap forward alignment score in linear space.
</li>
<li>
<b>SS_QG_FSQ</b> determines a quasiglobal gap forward alignment score in quadratic space.
</li>
<li>
<b>SS_QG_MATCH_PRINT</b> prints a quasiglobal gap alignment.
</li>
<li>
<b>SS_QG_MATCH_SCORE</b> scores a quasiglobal gap alignment.
</li>
<li>
<b>SS_QG_RPL</b> determines a quasiglobal gap recursive alignment path in linear space.
</li>
<li>
<b>SS_QG_RPL_POP</b> pops the data describing a subproblem off of the stack.
</li>
<li>
<b>SS_QG_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 29 December 2007.
</i>
<!-- John Burkardt -->
</body>
</html>