[med-svn] r12356 - in trunk/packages/conservation-code/trunk: . debian debian/patches debian/source
Laszlo Kajan
lkajan-guest at alioth.debian.org
Tue Oct 9 20:57:58 UTC 2012
Author: lkajan-guest
Date: 2012-10-09 20:57:58 +0000 (Tue, 09 Oct 2012)
New Revision: 12356
Added:
trunk/packages/conservation-code/trunk/debian/
trunk/packages/conservation-code/trunk/debian/README.source
trunk/packages/conservation-code/trunk/debian/changelog
trunk/packages/conservation-code/trunk/debian/compat
trunk/packages/conservation-code/trunk/debian/control
trunk/packages/conservation-code/trunk/debian/copyright
trunk/packages/conservation-code/trunk/debian/docs
trunk/packages/conservation-code/trunk/debian/examples
trunk/packages/conservation-code/trunk/debian/install
trunk/packages/conservation-code/trunk/debian/manpages
trunk/packages/conservation-code/trunk/debian/patches/
trunk/packages/conservation-code/trunk/debian/patches/examples
trunk/packages/conservation-code/trunk/debian/patches/manpage
trunk/packages/conservation-code/trunk/debian/patches/score_conservation
trunk/packages/conservation-code/trunk/debian/patches/series
trunk/packages/conservation-code/trunk/debian/rules
trunk/packages/conservation-code/trunk/debian/source/
trunk/packages/conservation-code/trunk/debian/source/format
trunk/packages/conservation-code/trunk/debian/upstream
Log:
packaging complete, tests out correctly
Property changes on: trunk/packages/conservation-code/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/conservation-code/trunk/debian/README.source
===================================================================
--- trunk/packages/conservation-code/trunk/debian/README.source (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/README.source 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1,14 @@
+conservation-code for Debian
+============================
+
+Repackaged Upstream Source
+--------------------------
+The 'get-orig-source' target is provided to build the upstream tarball.
+The problem with the upstream tarball is that it is not versioned. It also contains the main executable with extension (.py). In 'get-orig-source' the upstream tarball gets versioned and the extension of the executable is removed.
+
+Missing d/watch
+---------------
+Upstream (as of 20121009) does not version the downloadable tarball. There is a change log in the main executable, with dates. The latest date is used to form the version for the repacked upstream.
+A watch file will be created when upstream introduces version numbers to the name of the downloadable archive.
+
+# vim:et:ts=4:
Added: trunk/packages/conservation-code/trunk/debian/changelog
===================================================================
--- trunk/packages/conservation-code/trunk/debian/changelog (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/changelog 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1,5 @@
+conservation-code (20110309.0-1) UNRELEASED; urgency=low
+
+ * Initial release. (Closes: #690058)
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Tue, 09 Oct 2012 17:34:05 +0200
Added: trunk/packages/conservation-code/trunk/debian/compat
===================================================================
--- trunk/packages/conservation-code/trunk/debian/compat (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/compat 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1 @@
+8
Added: trunk/packages/conservation-code/trunk/debian/control
===================================================================
--- trunk/packages/conservation-code/trunk/debian/control (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/control 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1,43 @@
+Source: conservation-code
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Laszlo Kajan <lkajan at rostlab.org>
+Build-Depends: debhelper (>= 8.0.0)
+Standards-Version: 3.9.4
+Homepage: http://compbio.cs.princeton.edu/conservation/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/conservation-code/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/conservation-code/trunk/
+DM-Upload-Allowed: yes
+
+Package: conservation-code
+Architecture: all
+Depends: ${misc:Depends}, ${python:Depends}, python-numpy
+Enhances: concavity
+Description: protein sequence conservation scoring tool
+ This package provides score_conservation(1), a tool to score protein sequence
+ conservation.
+ .
+ The following conservation scoring methods are implemented:
+ * sum of pairs
+ * weighted sum of pairs
+ * Shannon entropy
+ * Shannon entropy with property groupings (Mirny and Shakhnovich 1995,
+ Valdar and Thornton 2001)
+ * relative entropy with property groupings (Williamson 1995)
+ * von Neumann entropy (Caffrey et al 2004)
+ * relative entropy (Samudrala and Wang 2006)
+ * Jensen-Shannon divergence (Capra and Singh 2007)
+ .
+ A window-based extension that incorporates the estimated conservation of
+ sequentially adjacent residues into the score for each column is also given.
+ This window approach can be applied to any of the conservation scoring
+ methods.
+ .
+ The program accepts alignments in the CLUSTAL and FASTA formats.
+ .
+ The sequence-specific output can be used as the conservation input for
+ concavity.
+ .
+ Conservation is highly predictive in identifying catalytic sites and
+ residues near bound ligands.
Added: trunk/packages/conservation-code/trunk/debian/copyright
===================================================================
--- trunk/packages/conservation-code/trunk/debian/copyright (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/copyright 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1,31 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: conservation_code
+Upstream-Contact: John A. Capra <tonyc at cs.princeton.edu>
+ Mona Singh <mona at cs.princeton.edu>
+Source: http://compbio.cs.princeton.edu/conservation/
+
+Files: debian/*
+Copyright: 2012 Laszlo Kajan <lkajan at rostlab.org>
+License: GPL-2.0+
+
+Files: *
+Copyright: Tony Capra 2007
+License: GPL-2.0+
+
+License: GPL-2.0+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
Added: trunk/packages/conservation-code/trunk/debian/docs
===================================================================
--- trunk/packages/conservation-code/trunk/debian/docs (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/docs 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1 @@
+README
Added: trunk/packages/conservation-code/trunk/debian/examples
===================================================================
--- trunk/packages/conservation-code/trunk/debian/examples (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/examples 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1 @@
+2plc__hssp-filtered.aln
Added: trunk/packages/conservation-code/trunk/debian/install
===================================================================
--- trunk/packages/conservation-code/trunk/debian/install (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/install 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1,3 @@
+distributions usr/share/conservation-code/
+matrix usr/share/conservation-code/
+score_conservation usr/bin/
Added: trunk/packages/conservation-code/trunk/debian/manpages
===================================================================
--- trunk/packages/conservation-code/trunk/debian/manpages (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/manpages 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1 @@
+score_conservation.1
Added: trunk/packages/conservation-code/trunk/debian/patches/examples
===================================================================
--- trunk/packages/conservation-code/trunk/debian/patches/examples (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/patches/examples 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1,41 @@
+--- /dev/null
++++ b/2plc__hssp-filtered.aln
+@@ -0,0 +1,38 @@
++CLUSTAL X (1.81) multiple sequence alignment
++
++
++2plc_ VTTKQWMSALPDTTNLAALSIPGTHDTMSYNGDITWTLTKPLAQTQTMSL
++Q9P866 VDYKTWLKDIDNNTRISKLSIPGTHNSAACHTAL------PSVQCQGASV
++Q59488 ITTKQWMSALPDNTKLTSLTIPGTHDTMSYKGNISWTLTKSLAQTQKMSL
++O07690 INTQRWMTSLPDSVSLSALSIPGTHDTMSYNGYITWQFTRPLAQTQTMTL
++PLC_LISMO VTTKQWMSALPDTTNLAALSIPGTHDTMSYNGDITWTLTKPLAQTQTMSL
++
++2plc_ YQQLEAGIRYIDIRAKDNLNIYHGPIFLNASLSGVLETITQFLKKNPKET
++Q9P866 TEQLEHGVRFLDIRVGKDLQVIHGKFPVKLKLKDTLEEVYKFLAHNSSET
++Q59488 FQQLEARIRYIDIRAKEDLQIYHGPIYLDASLKGVLETTVNFLKEHPKET
++O07690 NEQLNAGIRFFDIRAKEDLNIYHGPIYLNASLEEVLHTFISFLKENPKEV
++PLC_LISMO YQQLEAGIRYIDIRAKDNLNIYHGPIFLNASLSGVLETITQFLKKNPKET
++
++2plc_ IIMRLKDEQNSNDSFDYRIQPLINIYKDYFYTTPRTDTSNKIPTLKDVRG
++Q9P866 VIVSIKQEGNSQDEFGKLIWDYVNPNKDRWYLNT------DIPKLGDARG
++Q59488 IIMRLKDENNHNDRFDYRIQPLINQYKAFFYTTPKSDSSDKFPTLKELRG
++O07690 VIMRLKDENKSENSFDYRIQPLIHKLKSFFYTESAKNTSSKTPTLRKLRG
++PLC_LISMO IIMRLKDEQNSNDSFDYRIQPLINIYKDYFYTTPRTDTSNKIPTLKDVRG
++
++2plc_ KILLLSENHTKKPLVINSRKFGMQFGAPNQVIQDDYNGPSVKTKFKEIVQ
++Q9P866 KAILFRRFGVQDEQLKK--QFGFSASSWTYNTTNDDRGQFVVQDFCEVNT
++Q59488 KILLLLENGTNKPLTINYSKFGMKFAAENQVIQDNFNGPTIKTKYNEIVQ
++O07690 KILLLSDNNTKKSLVINSSRYGMQYDSSEQVIQDDYNGPDVNTKYQEIVQ
++PLC_LISMO KILLLSENHTKKPLVINSRKFGMQFGAPNQVIQDDYNGPSVKTKFKEIVQ
++
++2plc_ TAYQASKADNKLFLNHISATSLTFTPRQYAAALNNKVEQFVLNLTSEKVR
++Q9P866 ADDYTSKGDDKVFLNFTSASNFF---DQSCWPQPIAEAMIKGNIQETFHK
++Q59488 TAHQASSGENKLYLNHVSATSLTCTPYQYASTLNAKVDQYVTKLTAVGVR
++O07690 TAYQASSSENKLFLNYVSATSLTFTPSQYADKLNSKVENFVDNLTANKLN
++PLC_LISMO TAYQASKADNKLFLNHISATSLTFTPRQYAAALNNKVEQFVLNLTSEKVR
++
++2plc_ GLGILIMDFPEKQTIKNIIKNNKF
++Q9P866 GVGIIVLDYAETDNWK--------
++Q59488 GLGVFIMDFPPKQTIKSVIKNNKF
++O07690 GVGMLIMDFPEKQTIHSIIKNNKF
++PLC_LISMO GLGILIMDFPEKQTIKNIIKNNKF
Added: trunk/packages/conservation-code/trunk/debian/patches/manpage
===================================================================
--- trunk/packages/conservation-code/trunk/debian/patches/manpage (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/patches/manpage 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1,155 @@
+--- /dev/null
++++ b/score_conservation.1.pod
+@@ -0,0 +1,152 @@
++=pod
++
++=head1 NAME
++
++score_conservation - score protein sequence conservation
++
++=head1 SYNOPSIS
++
++score_conservation [options] ALIGNFILE
++
++=head1 DESCRIPTION
++
++Score protein sequence conservation in B<ALIGNFILE>. B<ALIGNFILE> must be in FASTA or CLUSTAL format.
++
++The following conservation scoring methods are implemented:
++ * sum of pairs
++ * weighted sum of pairs
++ * Shannon entropy
++ * Shannon entropy with property groupings (Mirny and Shakhnovich 1995,
++ Valdar and Thornton 2001)
++ * relative entropy with property groupings (Williamson 1995)
++ * von Neumann entropy (Caffrey et al 2004)
++ * relative entropy (Samudrala and Wang 2006)
++ * Jensen-Shannon divergence (Capra and Singh 2007)
++
++A window-based extension that incorporates the estimated conservation of
++sequentially adjacent residues into the score for each column is also given.
++This window approach can be applied to any of the conservation scoring
++methods.
++
++With default parameters score_conservation(1) computes the conservation scores for the alignment using the
++Jensen-Shannon divergence and a window B<-w> of I<3>.
++
++The sequence-specific output can be used as the conservation input for
++concavity.
++
++Conservation is highly predictive in identifying catalytic sites and
++residues near bound ligands.
++
++=head1 REFERENCES
++
++=over
++
++=item Capra JA and Singh M. Predicting functionally important residues from sequence conservation. Bioinformatics, 23(15):1875-82, 2007.
++
++=back
++
++=head1 OPTIONS
++
++=over
++
++=item -a [NAME]
++
++Reference sequence. Print scores in reference to the named sequence (ignoring gaps). Default prints the entire column.
++
++=item -b [0-1]
++
++Lambda for window heuristic linear combination. Default=I<.5>.
++
++Equation:
++
++C<score = (1 - lambda) * average_score_over_window_around_middle + lambda * score_of_middle>
++
++=item -d [FILE]
++
++Background distribution file, e.g. F<distributions/swissprot.distribution>. Default=built-in BLOSUM62.
++
++=item -g [0-1)]
++
++Gap cutoff. Do not score columns that contain more than gap cutoff fraction gaps. Default=I<.3>.
++
++=item -h
++
++Print help.
++
++=item -l [true|false]
++
++Use sequence weighting. Default=I<true>.
++
++=item -m [FILE]
++
++Similarity matrix file, e.g. F<matrix/blosum62.bla> or .qij. Default=F<matrix/blosum62.bla>.
++
++Some methods, e.g. I<js_divergence>, do not use this.
++
++=item -n [true|false]
++
++Normalize scores. Print the z-score (over the alignment) of each column raw score. Default=I<false>.
++
++=item -o FILE
++
++Output file. Default: standard output stream.
++
++=item -p [true|false]
++
++Use gap penalty. Lower the score of columns that contain gaps, proportionally to the sum weight of the gapped sequences. Default=I<true>.
++
++=item -s [METHOD]
++
++Conservation estimation method, one of I<shannon_entropy property_entropy property_relative_entropy vn_entropy relative_entropy js_divergence sum_of_pairs>. Default=I<js_divergence>.
++
++=item -w [0-INT]
++
++Window size. Number of residues on either side included in the window. Default=I<3>.
++
++=back
++
++=head1 EXAMPLES
++
++Note: you may have to copy and uncompress the example data files before running the following examples.
++
++=over
++
++=item Compute conservation scores for the alignment using the Jensen-Shannon divergence with default settings and print out the scores:
++
++ score_conservation __docdir__/examples/2plc__hssp-filtered.aln
++
++=item Score an alignment using Jensen-Shannon divergence, a window of size 3 (on either side of the residue), and the swissprot background distribution:
++
++ score_conservation -s js_divergence -w 3 -d \
++ __pkgdatadir__/distributions/swissprot.distribution \
++ __docdir__/examples/2plc__hssp-filtered.aln
++
++=back
++
++=head1 FILES
++
++=over
++
++=item Distributions
++
++F<__pkgdatadir__/distributions>
++
++=item Matrices
++
++F<__pkgdatadir__/matrix>
++
++=back
++
++=head1 SEE ALSO
++
++=over
++
++=item Homepage L<http://compbio.cs.princeton.edu/conservation/>
++
++=item Publication L<http://bioinformatics.oxfordjournals.org/cgi/content/full/23/15/1875>
++
++=item concavity(1)
++
++=back
++
++=cut
Added: trunk/packages/conservation-code/trunk/debian/patches/score_conservation
===================================================================
--- trunk/packages/conservation-code/trunk/debian/patches/score_conservation (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/patches/score_conservation 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1,46 @@
+--- a/score_conservation
++++ b/score_conservation
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python
+
+ ################################################################################
+ # score_conservation.py - Copyright Tony Capra 2007 - Last Update: 03/09/11
+@@ -98,7 +98,7 @@
+
+
+ def usage():
+- print """\nUSAGE:\npython score_conservation.py [options] alignfile\n\t -alignfile must be in fasta or clustal format.\n\nOPTIONS:\n\t
++ print """\nUSAGE:\nscore_conservation [options] alignfile\n\t -alignfile must be in fasta or clustal format.\n\nOPTIONS:\n\t
+ -a\treference sequence. Print scores in reference to a specific sequence (ignoring gaps). Default prints the entire column. [sequence name]\n\t
+ -b\tlambda for window heuristic linear combination. Default=.5 [real in [0,1]]\n
+ -d\tbackground distribution file, e.g., swissprot.distribution. Default=BLOSUM62 background [filename]\n\t
+@@ -136,8 +136,9 @@
+
+ aa_num += 1
+
++ freqsum = (sum(seq_weights) + len(amino_acids) * pc_amount)
+ for j in range(len(freq_counts)):
+- freq_counts[j] = freq_counts[j] / (sum(seq_weights) + len(amino_acids) * pc_amount)
++ freq_counts[j] = freq_counts[j] / freqsum
+
+ return freq_counts
+
+@@ -718,7 +719,7 @@
+ window_size = 3 # 0 = no window
+ win_lam = .5 # for window method linear combination
+ outfile_name = ""
+-s_matrix_file = "matrix/blosum62.bla"
++s_matrix_file = "/usr/share/conservation-code/matrix/blosum62.bla"
+ bg_distribution = blosum_background_distr[:]
+ scoring_function = js_divergence
+ use_seq_weights = True
+@@ -790,7 +791,7 @@
+ if arg == 'shannon_entropy': scoring_function = shannon_entropy
+ elif arg == 'property_entropy': scoring_function = property_entropy
+ elif arg == 'property_relative_entropy': scoring_function = property_relative_entropy
+- elif arg == 'vn_entropy': scoring_function = vn_entropy; from numarray import *; import numarray.linear_algebra as la
++ elif arg == 'vn_entropy': scoring_function = vn_entropy; from numpy.numarray import *; import numpy.numarray.linear_algebra as la
+
+ elif arg == 'relative_entropy': scoring_function = relative_entropy
+ elif arg == 'js_divergence': scoring_function = js_divergence
Added: trunk/packages/conservation-code/trunk/debian/patches/series
===================================================================
--- trunk/packages/conservation-code/trunk/debian/patches/series (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/patches/series 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1,3 @@
+examples
+manpage
+score_conservation
Added: trunk/packages/conservation-code/trunk/debian/rules
===================================================================
--- trunk/packages/conservation-code/trunk/debian/rules (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/rules 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1,51 @@
+#!/usr/bin/make -f
+#export DH_VERBOSE=1
+
+PACKAGE:=$(shell dpkg-parsechangelog --format rfc822|sed --posix -n -e 's/^Source: \(.*\)/\1/p;')
+VERSION:=$(shell dpkg-parsechangelog --format rfc822|sed --posix -n -e 's/^Version: \([0-9.]*\).*/\1/p;')
+
+MANS=score_conservation.1
+prefix?=/usr
+
+datarootdir:=${prefix}/share
+docdir:=${datarootdir}/doc/${PACKAGE}
+pkgdatadir:=${datarootdir}/${PACKAGE}
+
+.PHONY: get-orig-source
+get-orig-source:
+ set -e; \
+ if ! which xz; then \
+ echo "Could not find 'xz' tool for compression. Please apt-get install xz-utils." ; \
+ exit ; \
+ fi ; \
+ t=$$(mktemp -d) || exit 1; \
+ trap "rm -rf -- '$$t'" EXIT; \
+ pwd; \
+ o=conservation-code_$(VERSION).orig.tar; \
+ wget -O $$t/$${o}.gz http://compbio.cs.princeton.edu/conservation/conservation_code.tar.gz; \
+ ( cd "$$t"; \
+ gunzip *.tar.gz; \
+ tar --owner=root --group=root --mode=a+rX --delete -f *.tar --wildcards '*/.*'; \
+ tar --owner=root --group=root --mode=a+rX --extract -f *.tar; rm -f *.tar; \
+ mv conservation_code/score_conservation.py conservation_code/score_conservation; \
+ tar --owner=root --group=root --mode=a+rX --create -f $$o conservation_code; \
+ xz --best *.tar; \
+ ); \
+ mv $$t/*.tar.?z ./
+
+.PHONY: override_dh_auto_build-indep
+override_dh_auto_build-indep: man
+
+%:
+ dh $@ --parallel --with python2
+
+.PHONY: man
+man: $(MANS)
+
+%.1: %.1.pod
+ sed -e 's|__docdir__|$(docdir)|g;s|__pkgdatadir__|$(pkgdatadir)|g;s|__VERSION__|$(VERSION)|g;' "$<" | \
+ pod2man -c 'User Commands' -r "$(VERSION)" -name $(shell echo "$(basename $@)" | tr '[:lower:]' '[:upper:]') > "$@"
+
+.PHONY: override_dh_auto_clean
+override_dh_auto_clean:
+ rm -f $(MANS)
Property changes on: trunk/packages/conservation-code/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/conservation-code/trunk/debian/source/format
===================================================================
--- trunk/packages/conservation-code/trunk/debian/source/format (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/source/format 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/conservation-code/trunk/debian/upstream
===================================================================
--- trunk/packages/conservation-code/trunk/debian/upstream (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/upstream 2012-10-09 20:57:58 UTC (rev 12356)
@@ -0,0 +1,14 @@
+Name: conservation-code
+Contact: Tony Capra <http://compbio.cs.princeton.edu/conservation/>
+Homepage: http://compbio.cs.princeton.edu/conservation/
+Reference:
+ - Author: John A. Capra and Mona Singh
+ Title: Predicting functionally important residues from sequence conservation
+ Journal: Bioinformatics
+ Volume: 23
+ Number: 15
+ Pages: 1875-82
+ Year: 2007
+ URL: http://bioinformatics.oxfordjournals.org/content/23/15/1875.full
+ DOI: 10.1093/bioinformatics/btm270
+ PMID: 17519246
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