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[05/08/2014]Marine Dumousseau (marine@ebi.ac.uk)
Added parameters for consecutive locked nucleic acids and single mismatch in consecutive locked nucleic acids from Owczarzy et al. 2011
Updated version to 5.2.0
[23/05/2014]Marine Dumousseau (marine@ebi.ac.uk)
Fixed a bug in Locked nucleic acids formula which did not deal with terminal locked nucleic acids
Updated version to 5.1.2
[06/02/2014]Marine Dumousseau (marine@ebi.ac.uk)
Update documentation
Added batch script to run MELTING 5 with a file containing different sequences
[04/10/2013]William John Gowers (gowersj@babraham.ac.uk)
Added MELTING GUI for MELTING 5.x.
Updated version to 5.1.1
[09/08/2013]William John Gowers (gowersj@babraham.ac.uk)
Added new thermodynamic parameters for DNA/RNA duplexes from Watkins et al. (2010). Nucl. Acids Res. 39, 1894-1902.
[10/02/2013]Marine Dumousseau (marine@ebi.ac.uk)
Thanks to Richard Owczarzy:
Fixed typos in some thermodynamic parameters:
- bom00 model. GA/C- parameters are dH = -2.1 kcal/mol and dS = -3.9 in the paper
- san05 inosing model. Paramaters rounded to -6.0 kcal/mol. The paper reports -5.6 kcal/mol enthalpy.
- xia98 model. Parameters rounded into -6.8 kcal/mol. published -6.82 kcal/mol
- san04 bulge loop model. The sign of the entropy parameters are wrong.
- ser08 dangling ends model. The sign of some parameters (5' dangling ends) are wrong.
Added new GU parameters from from Serra et al., Biochemistry (2012) 51, 3508-3522. They are now the default parameters for GU base pairs.
version 5.1.0
[06/11/2012]Marine Dumousseau (marine@ebi.ac.uk)
Fix default path to NN files
version 5.0.6
[07/03/2012]Marine Dumousseau (marine@ebi.ac.uk)
Updated the documentation. The factor F cannot be 2 when the oligonucleotides are not self complementary and
one strand is in excess. In this case, F should be 1.
version 5.0.5
[07/01/2011]Marine Dumousseau (marine@ebi.ac.uk)
Changed the installation script
When melting is used without arguments, now displays the help
version 5.0.4
[02/11/2009] Marine Dumousseau (marine@ebi.ac.uk)
Changed the MELTING 5 documentations (references and acknoledgement)
Changed the files in the testResults folder.
version 5.0.3
[23/10/2009] Marine Dumousseau (marine@ebi.ac.uk)
Fixed some bugs in the inosine and single mismatch files.
Added other tests.
Changed the JAR File.
Fixed a bug for the hydroxyadenine model.
Put by 'all97' as default DNA Crick's pair thermodynamic model
version 5.0.2
[14/10/2009] Marine Dumousseau (marine@ebi.ac.uk)
Fixed some bugs in the melting.bib file.
version 5.0.1
[08/10/09] Marine Dumousseau (marine@ebi.ac.uk)
Fixed some bugs in the Javadoc.
Created a build.xml file and buildProject.sh to build the project.
[28/08/09] Marine Dumousseau (marine@ebi.ac.uk)
Fixed a bug for the option -O in OptionManagement.
Created the CompatibleMain class which allow a compatibility
between MELTING 4 and MELTING 5 options (except for the option '-q').
[17/08/09] Marine Dumousseau (marine@ebi.ac.uk)
Version 5 in Java.
New thermodynamic models and parameters for : Crick's pair,
single mismatch, tandem mismatch, internal loop, single
dangling end, double dangling end, long dangling end (only poly A),
inosine, hydroxyadenine, azobenzene, locked nucleic acids, single
bulge loop, long bulge loop.
New corrections for sodium, magnesium or mixed Na, Mg.
New corrections for DMSO and formamide.
[01/JUN/2009] Marine Dumousseau (marine@ebi.ac.uk)
tkmelting.1, tkmelting.1.xml and melting-gui.desktop added.
acknoledgements updated in the different documentation files.
version 4.3b
[15/APR/2009] Marine Dumousseau (marine@ebi.ac.uk)
mac executable added.
[14/APR/2009] Marine Dumousseau (marine@ebi.ac.uk)
Index.html added to the DOC folder.
linux 64 bits executable added.
[03/APR/2009] Marine Dumousseau (marine@ebi.ac.uk)
Documentation modified.
[31/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk)
mistakes in the thermodynamic tables corrected. Documentation
modification.
[31/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk)
inosine parameters added
[30/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk)
Perl interface bugs correction and move some files. Calcul.c and
melting.c bugs correction.
[27/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk)
Correction of the function which computes the fraction of GC base pairs.
We can now take in account the mismatches CXor GX and inosine mismatches
IG or IC.
New parameters of Santalucia added
[26/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk)
add the inosine parameters. (from Santalucia 2005 for DNA duplexes and
from Brent M. Znosko 2007 for RNA duplexes (only IU base pairs)).
add the option -i for enter a new set of inosine parameters.
version 4.3
[25/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk)
add the magnesium correction. (algorithm from Owczarzy 2008, only for
DNA/DNA duplexes)
add the options -k, -t, -G for the potassium, tris and magnesium
concentration.
The Tris+ concentration is about the half of total Tris concentration.
version 4.3
[24/MAR/2009] Marine Dumousseau (marine@ebi.ac.uk)
Fix mistakes in the calorimetric table sug95a.nn.
version 4.2i
[08/AUG/2007] Nicolas Le Novère (lenov@ebi.ac.uk)
Move from isolatin-1 to utf-8
version 4.2h
[06/SEP/2004] Nicolas Le Novère (lenov@ebi.ac.uk)
Fix mistakes in the calorimetric table xia98a.nn.
version 4.2g
[20/MAY/2004] Nicolas Le Novère (lenov@ebi.ac.uk)
Fix a mistake in the calorimetric table xia98a.nn. Thanks to Wong
Chee Hong (wongch@bii.a-star.edu.sg)
version 4.2f
[10/APR/2003] Nicolas Le Novère (lenov@pasteur.fr)
Minor modification of the verbose output.
version 4.2e
[11/FEB/2003] Nicolas Le Novère (lenov@pasteur.fr)
Modification of the documentation, regarding the correction of
strand concentration.
version 4.2d
[03/OCT/2002] Nicolas Le Novère (lenov@pasteur.fr)
Bug fix: An amazingly obvious mistake was introduced in the
approximate mode. The fractional GC was used instead of the
percent GC (Personnal view: The approximate mode is a crap
anyway).
version 4.2c
[14/MAY/2002] Nicolas Le Novère (lenov@pasteur.fr)
Bug fix: a break was forgotten in the big switch decoding the
options. Also the output of long messages did not comply with ISO
restrictions on string length. I split the strings. Thanks to
Mauro Petrillo.
version 4.2b
[18/FEB/2002] Nicolas Le Novère (lenov@pasteur.fr)
The threshold between exact and approximative computation is now
controlled by an option.
version 4.2
[14/FEB/2002] Nicolas Le Novère (lenov@pasteur.fr)
Correction of a typo in all97a.nn An entropic factor was changed
from -22.5 to -22.7 cal.M-1.K-1
version 4.1h
[19/NOV/2001] Nicolas Le Novère (lenov@pasteur.fr)
Corrections of the script profil.pl
version 4.1g
[18/MAY/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk)
Typographical mistake in decode.c:read_mm()
If the environment variable was undefined, or there was no
readable file at the specified place, the default defined at
compilation was not read.
Several minor editing of the error messages.
Modification of the Tk interface.
version 4.1f
[03/MAY/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk)
Big mistake in documentation (relative to the correction of
nucleic acid concentration). Took advantage to improve the
documentation (including benchmark results).
Minor correction of usage function.
version 4.1e
[29/APR/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk)
No need to enter a useless concentration of nucleic acid when
using the approximative mode. Small (but important) edit of the
script multi.pl. Addition of a benchmark in the directory TEST,
which compare various methods, NN sets, and salt corrections.
version 4.1d
[20/APR/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk)
Correction of several critical bugs in the reading of paramaeters
for mismatches and dangling ends. The format of the file containing the
parameters for mismatches is modified (the undetermined Crick's pair
were previously commented out. They are now included with parameters
equal to 99999).
version 4.1c
[10/APR/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk)
Correction of the code to prepare the implementation of dnarna and
rnarna mismatches and dangling ends. Correction of the makefile
for unices
version 4.1b
[29/MAR/2001] Nicolas Le Novère (nl223@cus.cam.ac.uk)
Implementation of the dangling ends analysis.
Addition of a several security corrections (strcpy -> strncpy,
check of malloc success ...).
Improvement of the makefile for Unices. Simplification of the
declaration of PATH for the nnfiles.
[07/AUG/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
version 4f. Mistakes in the NN file san96a.nn found by Leo
Schalkwyk
(l.schalkwyk@iop.kcl.ac.uk)
[05/JUN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
version 4e. Correction of the output to stderr et stdout (number
of spaces leading the lines). New perlTk interface.
[26/APR/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
version 4d. Typos in the code and the perl/Tk interface (unit of
entropy was given as J.Mol-1 instead J.Mol-1.K-1)
[24/APR/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
version 4c. Addition of a script (profil.pl) allowing an iterative
computation along a sequence, by sliding a window of a specified
width. Minor modifications of the documentation.
[09/FEB/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
version 4b. Some fixes of the program output and of the
documentation. Handle of the references in the parameter files
modified.
[08/FEB/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
MELTING4 release version. Corrections on the advice of Nicolas
Joly. Improved documentation.
[05/FEB/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
Changed the behaviour of options -v and -q. Improved
documentation.
[29/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
Fixed bugs in the interactive mode. Improved online help (option
-h). Fixed a lot of bugs or unpleasant features in the option
parsing. Changed the behaviour of options -A and -H. The former
has now always precedence over the latter regarding the et of NN
parameters.
[27/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
Second beta version. Correction of some NN files. Modifications of
documentation.
[26/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
First beta version. The program can now take in account mismatched
hybridisations. Correction of a bug in the screening of
Crick'pair.
[24/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
alpha5. The program can now read a file containing the
nearest-neighbor parameters for some mismatched Crick's pairs.
[18/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
on suggestion of Nicolas Joly (njoly@pasteur.fr) alpha3 and
alpha4. Code correction only.
[17/JAN/2000] Nicolas Le Novère (nl223@cus.cam.ac.uk)
alpha2. Modified the system to localize files containing set of nn
parameters. Now a directory is defined at compilation by
preprocessor directive. However, an environment variable can be
defined, which targets a directory where to find a nn file. If it
was not found there, it will be searched in the default
directory. Therefore, a user can define its own set of parameters,
while still using those installed with melting.
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