note070314

ls  sed -e 's/^\(.*\).fa/..\/hmmer\/binaries\/hmmpfam motif.hmm \1.fa > ..\/result\/\1.result/' sh

tar cf - whatever  ssh remotehost " ( cd /some/path ; tar xf - ) "
ssh -l ysc212 access3.cims.nyu.edu "( cd /tmp/mark ; tar cf - hmm ) "  tar xf -

tar cf - hmm  gzip  ssh -l ysc212 access3.cims.nyu.edu " ( cd /tmp/mark ; cat > hmm.tar.gz ) "



ls  sed -e 's/^\(.*\).fa/http:\/\/localhost:81\/sssdb\/tools\/motifseq10foldtest.php?motif=1A&fold=0\/

ls ../fa/*.fa  sed -e 's/^..\/fa\/\(.*\).fa/wget -O \1.fatr0 " http:\/\/192.168.1.100:81\/sssdb\/tools\/motifseq10foldtrain.php?motif=\1\&fold=0"/'
ls ../fa/*.fa  sed -e 's/^..\/fa\/\(.*\).fa/..\/muscle\/muscle3.6\/muscle -in \1.fatr0 -out \1.fatr0a/'
ls ../fa/*.fa  sed -e 's/^..\/fa\/\(.*\).fa/..\/hmmer\/binaries\/hmmbuild -g -n \1 -A motif.hmm \1.fatr0a/'
ls ../fa/*.fa  sed -e 's/^..\/fa\/\(.*\).fa/..\/hmmer\/binaries\/hmmpfam motif.hmm \1.fate0/'

ls ../fa/*.fa  sed -e 's/^..\/fa\/\(.*\).fa/..\/hmmer\/binaries\/hmmpfam -E 300 motif.hmm \1.fate0  perl ..\/fasta\/accuracy.pl \1/'  sh  perl ../fasta/totalaccuracy.pl
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yesrm *.fat*
rm motif.hmm
ls ../fa/*.fa  sed -e 's/^..\/fa\/\(.*\).fa/wget -O \1.fatr0 " http:\/\/192.168.1.100:81\/sssdb\/tools\/motifseq10foldtrain.php?motif=\1\&fold=0"/'
ls ../fa/*.fa  sed -e 's/^..\/fa\/\(.*\).fa/..\/muscle\/muscle3.6\/muscle -in \1.fatr0 -out \1.fatr0a/'
ls ../fa/*.fa  sed -e 's/^..\/fa\/\(.*\).fa/..\/hmmer\/binaries\/hmmbuild -g -n \1 -A motif.hmm \1.fatr0a/'
ls ../fa/*.fa  sed -e 's/^..\/fa\/\(.*\).fa/..\/hmmer\/binaries\/hmmpfam -E 300 motif.hmm \1.fate0  perl ..\/fasta\/accuracy.pl \1/'  sh  perl ../fasta/totalaccuracy.pl


for ($cx=0;$cx<10;$cx++){
  `yesrm *.fat*`;
  `rm motif.hmm`;
  `ls ../fa/*.fa  sed -e 's/^..\\/fa\\/\\(.*\\).fa/wget -q -O \\1.fatr$cx "http:\\/\\/192.168.1.100:81\\/sssdb\\/tools\\/motifseq10foldtrain.php?motif=\\1\\&fold=$cx"/'sh`;
  `ls ../fa/*.fa  sed -e 's/^..\\/fa\\/\\(.*\\).fa/wget -q -O \\1.fate$cx "http:\\/\\/192.168.1.100:81\\/sssdb\\/tools\\/motifseq10foldtest.php?motif=\\1\\&fold=$cx"/'sh`;
  `ls ../fa/*.fa  sed -e 's/^..\\/fa\\/\\(.*\\).fa/..\\/muscle\\/muscle3.6\\/muscle -quiet -in \\1.fatr$cx -out \\1.fatra$cx/'ish`;
  `ls ../fa/*.fa  sed -e 's/^..\\/fa\\/\\(.*\\).fa/..\\/hmmer\\/binaries\\/hmmbuild -g -n \\1 -A motif.hmm \\1.fatra$cx/'sh`;
  print `ls ../fa/*.fa  sed -e 's/^..\\/fa\\/\\(.*\\).fa/..\\/hmmer\\/binaries\\/hmmpfam -E 300 motif.hmm \\1.fate$cx  perl ..\\/fasta\\/accuracy.pl \\1/'  sh  perl ../fasta/totalaccuracy.pl`;
 
}

10fold
354/723

suggest 1B=1A
database wrong g6rlx.2
d1dyza_ suggest we should also train alpha helixes.
suggest d1nbqa2 should be 1F instead of 10C
this two suggest how HMM works: d1dyza_ & d1smaa1 & d1ea9c1
d1bf5a2 suggest we should see 7&8 as one (by seeing the sequence only, it knows 5&8 h-bonds together?)
three sheets like: d1ikna2(7F), d1nfia2(4F)
it can also suggest a way of transformation.
although HMM correctly identify d1tfpa_ is 38A, it also suggest d1tfpa_ is closed to 7J, as I comment in our database
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
38A.fa                                                  357.4   4.8e-106   1
7J.fa                                                   276.8      9e-82   1


detect 3 sheets, suggest g1pvc.1 is 6E, even g1pvc.1, d1du5a_ belongs to different fold:
NC: g1pvc.1: 6E.fa  346.5   9.2e-103        1
6E: d1du5a_, d1kwna_