• Reports
  contain the summary of our work.
  Report.6_6.ver3.2.equ0.200.davide
  Report.6_6.ver3.2.equ0.500.davide
  Report.6_6.ver3.2.equ2.200.davide
  Report.6_6.ver3.2.equ2.500.davide
  Report.7_7.ver3.1.equ2.200.davide
  Report.7_7.ver3.1.equ2.500.davide
  Report.7_7.ver3.2.equ0.200.davide
  Report.7_7.ver3.2.equ0.500.davide
  Report.8_8.ver3.1.equ2.200.davide
  Report.8_8.ver3.1.equ2.500.davide
  Report.8_8.ver3.2.equ0.200.davide
  Report.8_8.ver3.2.equ0.500.davide
  
  A sample entry taken from Report.6_6.ver3.2.equ0.200.davide is

  ----------------------------------------------------------------------
  CATACA_ATATAC
  ratio=1.5
  CATACA  ATATAC  183     156     61      500     11177   18446744073709551615    2089    0.0000157224
  NO: it does not pass the GO filter
  ratio=1.2
  CATACA  ATATAC  183     156     61      500     11177   18446744073709551615    1629    0.0000122603
  NO: it does not pass the GO filter
  

  This means that we have found the couple CATACA_ATATAC ( with equivalence EQU0 ) and that it has been found for ratio =1.2 and 1.5 .
  The line

  CATACA  ATATAC  183     156     61      500     11177   18446744073709551615    2089    0.0000157224
  

  mean that the couple has 183 occurences in 156 upstreams when we have considered upstreams of up to 500bp and a sliding window of 200bp .
  Its average distance is of 61bp, a variation of distance of 500bp (this means that it has not be computed),
  The actual sum of all distances is 11177bp, the actual sum of all squared distances is 1844674407370955161 ( not computed)
  The Bonferroni corrected P-value computed from the distance distribution is 0.0000157224 and the number of genes with 183 occurences is 2089 (this datum is needed for computing the Bonferroni correction).
  The sentence "NO: it does not pass the GO filter" means that this couple has not passed the GO filter.
  
  Finally the following example taken from Report.8_8.ver3.1.equ2.500.davide

  ----------------------------------------------------------------------
  AGCTCATC_AAAAGAAA
  ratio=1.5
  AGCTCATC        AAAAGAAA        90      65      87      500     7874    18446744073709551615    622     0.0000013450
  AGCTCATC_AAAAGAAA.equ2  GO:0005730      6591    217     65      20      14.144182       nucleolus       C
  AGCTCATC_AAAAGAAA.equ2  GO:0007046      6591    190     65      19      14.066939       ribosome biogenesis     P
  AGCTCATC_AAAAGAAA.equ2  GO:0042254      6591    230     65      20      13.653928       ribosome biogenesis and assembly
          P
  AGCTCATC_AAAAGAAA.equ2  GO:0007028      6591    230     65      20      13.653928       cytoplasm organization and biogenesi
  s       P
  AGCTCATC_AAAAGAAA.equ2  GO:0016072      6591    165     65      15      10.453190       rRNA metabolism P
  AGCTCATC_AAAAGAAA.equ2  GO:0006364      6591    159     65      14      9.571413        rRNA processing P
  AGCTCATC_AAAAGAAA.equ2  GO:0016070      6591    430     65      19      7.820250        RNA metabolism  P
  AGCTCATC_AAAAGAAA.equ2  GO:0005634      6591    1794    65      39      7.582947        nucleus C
  AGCTCATC_AAAAGAAA.equ2  GO:0042255      6591    60      65      8       7.007824        ribosome assembly       P
  AGCTCATC_AAAAGAAA.equ2  GO:0043232      6591    830     65      25      6.996922        intracellular non-membrane-bound org
  anelle  C
  AGCTCATC_AAAAGAAA.equ2  GO:0043228      6591    830     65      25      6.996922        non-membrane-bound organelle    C
  AGCTCATC_AAAAGAAA.equ2  GO:0006396      6591    318     65      15      6.527469        RNA processing  P
  AGCTCATC_AAAAGAAA.equ2  GO:0042257      6591    50      65      7       6.331148        ribosomal subunit assembly      P
  

Glossary

• EQU0
  For example the equivalence class for the couple (AC,CT) is given by {(AC,CT), (AG,GT)} .
• EQU2
  For example the equivalence class for the couple (AC,CT) is given by { (AC,CT), (GT,CT) , (AC,AG) , (GT,AG) , (CT,AC), (CT,GT) , (AG,AC) , (AG,GT) }.
• ratio
  We define ratio the ratio between the number of occurences of a given couple of words and the number of upstreams where the given couple is found.