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smoe eliza-m

ffindex_soedinglab's Issues

Separate git repo for mpq library?

Hello,

while compiling hhsuite with openmpi installed, I ran into an error because of a missing mpq library that you ship with ffindex. I then quickly deinstalled openmpi, but the better approach may be to offer the header file and the library to link against. Would you accept a patch against ffindex to create respective library? Or is there another git repository for mpq out there somewhere? Should there be one? In #4 I already learned that you treat
ffindex as a git subproject, which completely explains why you don't run into any such issue on your side since you have everything in one tree. But the users of yours who compile from your hhsuite release source tree will notice since ffindex is then external to that tree, which is just the right way how it should be for the redistribution. Just, somehow, mpq is a bit lost.

Cheers,

Steffen

Please create releases to sync with hhsuite

Hello,

I found ffsort_ not to be available in what Laszlo previously retrieved from http://www.splashground.de/~andy/programs/FFindex/ . It is apparently needed for the hhsuite 3 beta releases. Some googling guided me here.

Cheers,

Steffen

Zero secondary structure when using both pdb and pfam

Hi,

When using both pdb and pfam:

hhsearch -d /home/ucgajhe/levine/databases/pdb70/pdb70 -ssm 4 -cpu 12 -o /home/ucgajhe/Scratch/Levine/results/test_YPR199C/YPR199C.0.ssw11.hhr -i /home/ucgajhe/Scratch/Levine/results/test_YPR199C/YPR199C.0.ss.a3m -v 2 -p 0 -cov 50 -ssw 0.11 -Z 5000 -d /home/ucgajhe/levine/databases/pfamA_30/pfam

we observe zero secondary structure scores for both PDB matches and PFAM matches:

No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 1gd2_E Transcription factor PA  98.7 3.4E-10 6.3E-15   83.8   8.4   68   11-81      1-68  (70)
  2 1sse_B AP-1 like transcription  98.7 2.3E-11 4.2E-16   97.0   0.0   60  235-294    26-85  (86)
  3 1gu4_A CAAT/enhancer binding p  98.1 2.5E-07 4.5E-12   69.3   9.7   61   14-77     11-71  (78)
  4 PF08601.7 ; PAP1 ; Transcripti  97.9   3E-08 5.5E-13   97.1   0.0   56  236-291   298-355 (356)
  5 1hjb_A Ccaat/enhancer binding   97.7   1E-07 1.9E-12   73.4   0.0   61   15-78     12-72  (87)
  6 1ci6_A Transcription factor AT  97.5 2.9E-07 5.3E-12   65.6   0.0   57   18-77      2-58  (63)
  7 PF00170.18 ; bZIP_1 ; bZIP tra  97.5 3.5E-07 6.5E-12   64.3   0.0   58   18-78      5-62  (64)
  8 2dgc_A Protein (GCN4); basic d  97.5 4.4E-07   8E-12   64.4   0.0   57   15-74      6-62  (63)
  9 2wt7_A Proto-oncogene protein   97.4 6.9E-07 1.3E-11   63.0   0.0   57   18-77      2-58  (63)
 10 1jnm_A Proto-oncogene C-JUN; B  97.3 1.2E-06 2.2E-11   61.0   0.0   57   19-78      2-58  (62)
 11 1dh3_A Transcription factor CR  97.2 1.7E-06 3.1E-11   59.9   0.0   52   19-73      2-53  (55)
 12 PF07716.12 ; bZIP_2 ; Basic re  97.1 2.7E-06 4.9E-11   58.3   0.0   51   17-70      4-54  (55)
 13 1t2k_D Cyclic-AMP-dependent tr  97.1 2.8E-06 5.2E-11   59.0   0.0   55   19-76      2-56  (61)
 14 3a5t_A Transcription factor MA  97.1   4E-06 7.2E-11   68.2   0.0   62   18-82     37-98  (107)
 15 2wt7_B Transcription factor MA  97.0 6.5E-06 1.2E-10   64.3   0.0   60   18-80     27-86  (90)
 16 PF03131.14 ; bZIP_Maf ; bZIP M  96.9 9.6E-06 1.8E-10   62.1   0.0   58   18-78     30-87  (90)
 17 5apu_A General control protein  96.5 0.00019 3.5E-09   59.1   3.2   48   19-73     46-93  (95)
 18 2oxj_A Hybrid alpha/beta pepti  94.6   0.029 5.3E-07   38.0   4.4   32   39-73      1-32  (34)
 19 2r2v_A GCN4 leucine zipper; co  94.4   0.036 6.6E-07   38.0   4.2   32   39-73      1-32  (34)
 20 PF16689.2 ; APC_N_CC ; Coiled-  94.2  0.0059 1.1E-07   44.5   0.0   43   39-84      1-43  (52)
 21 4c46_A General control protein  94.0  0.0079 1.4E-07   47.9   0.0   51   18-72     26-76  (76)
 22 1kd8_B GABH BLL, GCN4 acid bas  93.7   0.011   2E-07   41.0   0.0   35   39-76      1-35  (36)
 23 3w92_A Thioester coiled coil p  93.3   0.015 2.8E-07   39.4   0.0   31   40-73      1-31  (32)
 24 1deb_A APC protein, adenomatou  93.3   0.015 2.8E-07   43.2   0.0   43   38-83      2-44  (54)
 25 2wq1_A General control protein  92.6   0.025 4.5E-07   38.6   0.0   31   40-73      1-31  (33)
 26 3c3g_A Alpha/beta peptide with  92.3    0.03 5.4E-07   38.2   0.0   31   40-73      1-31  (33)

but when running with PDB only, we get nonzero scores for all matches.

I note that the PDB database download includes SS data, but PFAM does not. But this doesn't explain why we are getting zero SS scores for the PDB hits when PFAM is present:


No 10
>2dgc_A Protein (GCN4); basic domain, leucine zipper, DNA binding, eukaryotic regulatory protein, transcription/DNA complex; HET: DNA; 2.20A {Saccharomyces cerevisiae} SCOP: h.1.3.1 PDB: 1dgc_A* 1ld4_E 1ysa_C* 3p8m_D
Probab=97.47  E-value=4.4e-07  Score=64.37  Aligned_cols=57  Identities=26%  Similarity=0.323  Sum_probs=45.1  Template_Neff=9.500

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q YPR199C          15 LTPPKNKRAAQLRASQNAFRKRKLERLEELEKKEAQLTVTNDQIHILKKENELLHFMLRS   74 (294)
Q Consensus        15 ~~~~k~KRKaQNRaAQkAFRERKE~rlkeLE~kl~ele~~~~~~~~L~~EnE~Lr~~n~e   74 (294)
                      ....+.+|+.+||.||+.+|+||..++.+||.++..|+..+   ..|..+++.|+..+..
T Consensus         6 ~~~~~~~kr~rnr~~~~~~R~rk~~~~~~le~~v~~l~~~~---~~l~~~~~~l~~~~~~   62 (63)
T 2dgc_A            6 SSDPAALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKN---YHLENEVARLKKLVGE   62 (63)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHC---
T ss_pred             cccHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHh
Confidence            34566778899999999999999999999999999999888   7888888888876654


No 11
>PF00170.19 ; bZIP_1 ; bZIP transcription factor
Probab=97.45  E-value=4.9e-07  Score=63.79  Aligned_cols=58  Identities=28%  Similarity=0.290  Sum_probs=51.1  Template_Neff=9.800

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q YPR199C          18 PKNKRAAQLRASQNAFRKRKLERLEELEKKEAQLTVTNDQIHILKKENELLHFMLRSLLTE   78 (294)
Q Consensus        18 ~k~KRKaQNRaAQkAFRERKE~rlkeLE~kl~ele~~~~~~~~L~~EnE~Lr~~n~el~~e   78 (294)
                      ++.+|+.+||.||+.||+||..++.+||.++..|+...   ..|..+++.|+..+..|..+
T Consensus         5 k~~rr~~~nr~~~~~~R~rk~~~~~~Le~~~~~L~~~~---~~l~~~~~~l~~e~~~L~~~   62 (64)
T GBF1_ARATH/220    5 KRQKRKQSNRESARRSRLRKQAECEQLQQRVESLSNEN---QSLRDELQRLSSECDKLKSE   62 (64)
Confidence            56788999999999999999999999999999999888   77888888888887776554

We note that secondary structure nonzero matches are found in the web-search tool, but that the downloadable version of hh-pfam does not have any SS info in it.

Most confusing of all, though, is why PDB matches become zero SS score when PFAM is present.

I think this might have something to do with the code in https://github.com/soedinglab/hh-suite/blob/master/src/hhviterbirunner.cpp

   int ss_hmm_mode = HMM::computeScoreSSMode(q_simd->GetHMM(0), t_hmm_simd->GetHMM(0));
    for(size_t i = 1; i < maxres; i++){
        ss_hmm_mode = std::min(ss_hmm_mode,
                               HMM::computeScoreSSMode(q_simd->GetHMM(0), t_hmm_simd->GetHMM(i)));
    }

and this:

https://github.com/soedinglab/hh-suite/blob/master/src/hhhmm.cpp

int HMM::computeScoreSSMode( HMM *q,  HMM *t){
	int returnMode = HMM::NO_SS_INFORMATION;
	if      (q->nss_pred>=0 && t->nss_dssp>=0) returnMode=HMM::PRED_DSSP;
	else if (q->nss_dssp>=0 && t->nss_pred>=0) returnMode=HMM::DSSP_PRED;
	else if (q->nss_pred>=0 && t->nss_pred>=0) returnMode=HMM::PRED_PRED;
	return returnMode;
}

which takes a minimum across the available data, so would result in zero SS for PDB when PFAM is present.

Any thoughts?

ffindex_from_fasta.c needs author information

ffindex_from_fasta.c is heavily modified.
The file clearly states:
" * Please add your name here if you distribute modified versions. "

ffindex_modify segfaults during tests

Hi,
I just learned in Issue 4 that I might have grabbed the wrong codebase for Debian when I pointed it to this Git repository. However, you might be interested to know that ffindex_modify segfaults in our test suite which you can see in the Debian bug report.
Hope this helps, Andreas.

FFindex trademark notification

FFindex is a trademark of the Ludwig-Maximilians-Universität München.

Please update your documentation accordingly.

Herzliche Grüße
Andreas Hauser

Install problem

Hi, I'm trying to package hh-suite for GNU Guix but running into the following problem trying to install this ffindex fork. Any ideas?

ben@ben /tmp/ffindex_soedinglab/build [env]# cmake -DCMAKE_INSTALL_PREFIX=/tmp -DCMAKE_BUILD_TYPE=RelWithDebInfo -G "Unix Makefiles" ..
-- The C compiler identification is GNU 4.9.4
-- Check for working C compiler: /gnu/store/5bakywgsavpc21zbli8hqq9qgrladcjn-profile/bin/gcc
-- Check for working C compiler: /gnu/store/5bakywgsavpc21zbli8hqq9qgrladcjn-profile/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for fmemopen
-- Looking for fmemopen - found
-- Found MPI_C: /gnu/store/5bakywgsavpc21zbli8hqq9qgrladcjn-profile/lib/libmpi.so  
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/ffindex_soedinglab/build
ben@ben /tmp/ffindex_soedinglab/build [env]# make
Scanning dependencies of target ffindex
[  3%] Building C object src/CMakeFiles/ffindex.dir/ffindex.c.o
[  7%] Building C object src/CMakeFiles/ffindex.dir/ffutil.c.o
[ 11%] Linking C static library libffindex.a
[ 11%] Built target ffindex
Scanning dependencies of target ffindex_from_fasta_with_split
[ 15%] Building C object src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o
[ 19%] Linking C executable ffindex_from_fasta_with_split
[ 19%] Built target ffindex_from_fasta_with_split
Scanning dependencies of target ffindex_modify
[ 23%] Building C object src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o
[ 26%] Linking C executable ffindex_modify
[ 26%] Built target ffindex_modify
Scanning dependencies of target mpq
[ 30%] Building C object src/mpq/CMakeFiles/mpq.dir/mpq.c.o
[ 34%] Linking C static library libmpq.a
[ 34%] Built target mpq
Scanning dependencies of target ffindex_apply_mpi
[ 38%] Building C object src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o
[ 42%] Linking C executable ffindex_apply_mpi
[ 42%] Built target ffindex_apply_mpi
Scanning dependencies of target ffindex_apply
[ 46%] Building C object src/CMakeFiles/ffindex_apply.dir/ffindex_apply.c.o
[ 50%] Linking C executable ffindex_apply
[ 50%] Built target ffindex_apply
Scanning dependencies of target ffindex_build
[ 53%] Building C object src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o
[ 57%] Linking C executable ffindex_build
[ 57%] Built target ffindex_build
Scanning dependencies of target ffindex_from_fasta
[ 61%] Building C object src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o
[ 65%] Linking C executable ffindex_from_fasta
[ 65%] Built target ffindex_from_fasta
Scanning dependencies of target ffindex_shared
[ 69%] Building C object src/CMakeFiles/ffindex_shared.dir/ffindex.c.o
[ 73%] Building C object src/CMakeFiles/ffindex_shared.dir/ffutil.c.o
[ 76%] Linking C shared library libffindex_shared.so
[ 76%] Built target ffindex_shared
Scanning dependencies of target ffindex_unpack
[ 80%] Building C object src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o
[ 84%] Linking C executable ffindex_unpack
[ 84%] Built target ffindex_unpack
Scanning dependencies of target ffindex_get
[ 88%] Building C object src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o
[ 92%] Linking C executable ffindex_get
[ 92%] Built target ffindex_get
Scanning dependencies of target ffindex_order
[ 96%] Building C object src/CMakeFiles/ffindex_order.dir/ffindex_order.c.o
[100%] Linking C executable ffindex_order
[100%] Built target ffindex_order
ben@ben /tmp/ffindex_soedinglab/build [env]# make install
[ 11%] Built target ffindex
[ 19%] Built target ffindex_from_fasta_with_split
[ 26%] Built target ffindex_modify
[ 34%] Built target mpq
[ 42%] Built target ffindex_apply_mpi
[ 50%] Built target ffindex_apply
[ 57%] Built target ffindex_build
[ 65%] Built target ffindex_from_fasta
[ 76%] Built target ffindex_shared
[ 84%] Built target ffindex_unpack
[ 92%] Built target ffindex_get
[100%] Built target ffindex_order
Install the project...
-- Install configuration: "RelWithDebInfo"
CMake Error at src/cmake_install.cmake:36 (file):
  file INSTALL cannot find "//ffindex_apply_mpi".
Call Stack (most recent call first):
  cmake_install.cmake:37 (include)

Thanks.

Please rename your fork

Hi,

please either use the offical github:
https://github.com/ahcm/ffindex
or rename your fork.

Cheers
Andy

soedinglab / ffindex_soedinglab Goto Github PK

ffindex_soedinglab's People

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Watchers

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ffindex_soedinglab's Issues

Separate git repo for mpq library?

Please create releases to sync with hhsuite

Zero secondary structure when using both pdb and pfam

ffindex_from_fasta.c needs author information

ffindex_modify segfaults during tests

FFindex trademark notification

Install problem

Please rename your fork

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