Le Thu, Jan 03, 2008 at 01:01:45PM -0500, Benjamin Redelings a écrit :
>
> The probcons package contains a binary probcons-RNA that is very
> different than the one that is provided at this page:
>
> http://probcons.stanford.edu/download.html
>
> It gives very different result when applied to a collection of diverse
> 5S RNAs, producing a huge alignment that is mostly gaps. Attempts to
> train it (using the -t option) produce a parameter file that contains an
> amino-acid transition matrix, NOT a nucleic-acid transition matrix.
Dear Benjamin, many thanks for the report.
Apparently something is going wrong in the building of probconsRNA. The version
provided upstream is 1.10, whereas probcons iteslf is now 1.12. In Debian, we
build probconsRNA from probcons 1.12. I attached the the difference between
probcons 1.10 and probconsRNA 1.10. As you can see, only Defaults.h and the
Makefile differ. Therefore, instead of using the original sources of
probconsRNA, we ship Defaults.h, renamed DefaultsRNA.h, copy Main.cc as
MainRNA.cc, and build probconsRNA with the rest of the probcons sources version
1.12. (see the following patch for the details:)
http://svn.debian.org/wsvn/debian-med/trunk/packages/probcons/trunk/debian/patches/10_add-RNA-in-Makefile.diff?op=file&rev=0&sc=0
Can you provide me your sequence files so that we have a common
reference ?
Have a nice day,
--
Charles Plessy
Debian-med packaging team.
Wakō, Saitama, Japan
diff -u probcons/Defaults.h probconsRNA/Defaults.h
--- probcons/Defaults.h 2004-07-13 23:04:34.000000000 +0200
+++ probconsRNA/Defaults.h 2005-06-07 23:27:54.000000000 +0200
@@ -15,49 +15,26 @@
using namespace std;
-/*
-float initDistrib1Default[] = { 0.3202854395, 0.3398572505, 0.3398572505 };
-float gapOpen1Default[] = { 0.1375414133, 0.1375414133 };
-float gapExtend1Default[] = { 0.7832147479, 0.7832147479 };
-*/
-
-float initDistrib1Default[] = { 0.6080327034f, 0.1959836632f, 0.1959836632f };
-float gapOpen1Default[] = { 0.01993141696f, 0.01993141696f };
-float gapExtend1Default[] = { 0.7943345308f, 0.7943345308f };
-
-float initDistrib2Default[] = { 0.6814756989f, 8.615339902e-05f, 8.615339902e-05f, 0.1591759622f, 0.1591759622 };
-float gapOpen2Default[] = { 0.0119511066f, 0.0119511066f, 0.008008334786f, 0.008008334786 };
-float gapExtend2Default[] = { 0.3965826333f, 0.3965826333f, 0.8988758326f, 0.8988758326 };
-
-string alphabetDefault = "ARNDCQEGHILKMFPSTWYV";
-float emitSingleDefault[20] = {
- 0.07831005f, 0.05246024f, 0.04433257f, 0.05130349f, 0.02189704f,
- 0.03585766f, 0.05615771f, 0.07783433f, 0.02601093f, 0.06511648f,
- 0.09716489f, 0.05877077f, 0.02438117f, 0.04463228f, 0.03940142f,
- 0.05849916f, 0.05115306f, 0.01203523f, 0.03124726f, 0.07343426f
+float initDistrib1Default[] = { 0.9588437676f, 0.0205782652f, 0.0205782652f };
+float gapOpen1Default[] = { 0.0190259293f, 0.0190259293f };
+float gapExtend1Default[] = { 0.3269913495f, 0.3269913495f };
+
+float initDistrib2Default[] = { 0.9615409374f, 0.0000004538f, 0.0000004538f, 0.0192291681f, 0.0192291681f };
+float gapOpen2Default[] = { 0.0082473317f, 0.0082473317f, 0.0107844425f, 0.0107844425f };
+float gapExtend2Default[] = { 0.3210460842f, 0.3210460842f, 0.3298229277f, 0.3298229277f };
+
+string alphabetDefault = "ACGUTN";
+float emitSingleDefault[6] = {
+ 0.2270790040f, 0.2422080040f, 0.2839320004f, 0.2464679927f, 0.2464679927f, 0.0003124650f
};
-float emitPairsDefault[20][20] = {
- {0.02373072f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00244502f, 0.01775118f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00210228f, 0.00207782f, 0.01281864f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00223549f, 0.00161657f, 0.00353540f, 0.01911178f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00145515f, 0.00044701f, 0.00042479f, 0.00036798f, 0.01013470f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00219102f, 0.00253532f, 0.00158223f, 0.00176784f, 0.00032102f, 0.00756604f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00332218f, 0.00268865f, 0.00224738f, 0.00496800f, 0.00037956f, 0.00345128f, 0.01676565f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00597898f, 0.00194865f, 0.00288882f, 0.00235249f, 0.00071206f, 0.00142432f, 0.00214860f, 0.04062876f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00114353f, 0.00132105f, 0.00141205f, 0.00097077f, 0.00026421f, 0.00113901f, 0.00131767f, 0.00103704f, 0.00867996f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00318853f, 0.00138145f, 0.00104273f, 0.00105355f, 0.00094040f, 0.00100883f, 0.00124207f, 0.00142520f, 0.00059716f, 0.01778263f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00449576f, 0.00246811f, 0.00160275f, 0.00161966f, 0.00138494f, 0.00180553f, 0.00222063f, 0.00212853f, 0.00111754f, 0.01071834f, 0.03583921f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00331693f, 0.00595650f, 0.00257310f, 0.00252518f, 0.00046951f, 0.00312308f, 0.00428420f, 0.00259311f, 0.00121376f, 0.00157852f, 0.00259626f, 0.01612228f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00148878f, 0.00076734f, 0.00063401f, 0.00047808f, 0.00037421f, 0.00075546f, 0.00076105f, 0.00066504f, 0.00042237f, 0.00224097f, 0.00461939f, 0.00096120f, 0.00409522f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00165004f, 0.00090768f, 0.00084658f, 0.00069041f, 0.00052274f, 0.00059248f, 0.00078814f, 0.00115204f, 0.00072545f, 0.00279948f, 0.00533369f, 0.00087222f, 0.00116111f, 0.01661038f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00230618f, 0.00106268f, 0.00100282f, 0.00125381f, 0.00034766f, 0.00090111f, 0.00151550f, 0.00155601f, 0.00049078f, 0.00103767f, 0.00157310f, 0.00154836f, 0.00046718f, 0.00060701f, 0.01846071f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00631752f, 0.00224540f, 0.00301397f, 0.00285226f, 0.00094867f, 0.00191155f, 0.00293898f, 0.00381962f, 0.00116422f, 0.00173565f, 0.00250962f, 0.00312633f, 0.00087787f, 0.00119036f, 0.00180037f, 0.01346609f, 0.0f, 0.0f, 0.0f, 0.0f},
- {0.00389995f, 0.00186053f, 0.00220144f, 0.00180488f, 0.00073798f, 0.00154526f, 0.00216760f, 0.00214841f, 0.00077747f, 0.00248968f, 0.00302273f, 0.00250862f, 0.00093371f, 0.00107595f, 0.00147982f, 0.00487295f, 0.01299436f, 0.0f, 0.0f, 0.0f},
- {0.00039119f, 0.00029139f, 0.00021006f, 0.00016015f, 0.00010666f, 0.00020592f, 0.00023815f, 0.00038786f, 0.00019097f, 0.00039549f, 0.00076736f, 0.00028448f, 0.00016253f, 0.00085751f, 0.00015674f, 0.00026525f, 0.00024961f, 0.00563625f, 0.0f, 0.0f},
- {0.00131840f, 0.00099430f, 0.00074960f, 0.00066005f, 0.00036626f, 0.00070192f, 0.00092548f, 0.00089301f, 0.00131038f, 0.00127857f, 0.00219713f, 0.00100817f, 0.00054105f, 0.00368739f, 0.00047608f, 0.00102648f, 0.00094759f, 0.00069226f, 0.00999315f, 0.0f},
- {0.00533241f, 0.00169359f, 0.00136609f, 0.00127915f, 0.00119152f, 0.00132844f, 0.00178697f, 0.00194579f, 0.00071553f, 0.01117956f, 0.00914460f, 0.00210897f, 0.00197461f, 0.00256159f, 0.00135781f, 0.00241601f, 0.00343452f, 0.00038538f, 0.00148001f, 0.02075171f}
+float emitPairsDefault[6][6] = {
+ { 0.1487240046f, 0.0184142999f, 0.0361397006f, 0.0238473993f, 0.0238473993f, 0.0000375308f },
+ { 0.0184142999f, 0.1583919972f, 0.0275536999f, 0.0389291011f, 0.0389291011f, 0.0000815823f },
+ { 0.0361397006f, 0.0275536999f, 0.1979320049f, 0.0244289003f, 0.0244289003f, 0.0000824765f },
+ { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
+ { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
+ { 0.0000375308f, 0.0000815823f, 0.0000824765f, 0.0000743985f, 0.0000743985f, 0.0000263252f }
};
#endif
Only in probconsRNA: Defaults.h~
diff -u probcons/Makefile probconsRNA/Makefile
--- probcons/Makefile 2005-04-21 20:54:59.000000000 +0200
+++ probconsRNA/Makefile 2005-06-07 20:43:53.000000000 +0200
@@ -15,7 +15,7 @@
# c) RELEASE mode
################################################################################
-OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.10"
+OTHERFLAGS = -DNumInsertStates=1 -DVERSION="1.10"
# debug mode
#CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)
Only in probconsRNA: Makefile~
Only in probconsRNA: compare
Only in probconsRNA: makegnuplot
Only in probconsRNA: mlparams0
Only in probconsRNA: mlparams0~
Only in probconsRNA: params-weird
Only in probconsRNA: params0
Only in probconsRNA: params1
Only in probconsRNA: params10
Only in probconsRNA: params11
Only in probconsRNA: params12
Only in probconsRNA: params13
Only in probconsRNA: params14
Only in probconsRNA: params15
Only in probconsRNA: params16
Only in probconsRNA: params17
Only in probconsRNA: params18
Only in probconsRNA: params19
Only in probconsRNA: params2
Only in probconsRNA: params20
Only in probconsRNA: params21
Only in probconsRNA: params22
Only in probconsRNA: params23
Only in probconsRNA: params24
Only in probconsRNA: params25
Only in probconsRNA: params26
Only in probconsRNA: params27
Only in probconsRNA: params28
Only in probconsRNA: params29
Only in probconsRNA: params3
Only in probconsRNA: params30
Only in probconsRNA: params4
Only in probconsRNA: params5
Only in probconsRNA: params6
Only in probconsRNA: params7
Only in probconsRNA: params8
Only in probconsRNA: params9
Only in probconsRNA: probcons
Only in probconsRNA: project
Only in probconsRNA: train-script
Only in probconsRNA: train-script~
