Description

The DNAELE record contains the coordinate information for any other biological element associated with DNA, whether this element is bound to DNA or free to diffuse in the nucleus. There is also the information of the variance of the spatial distribution observed for this locus.

Record Format

COLUMNS        DATA  TYPE    FIELD        DEFINITION
-------------------------------------------------------------------------------------
 1 -  6        Record name   "DNAELE"
 8 - 15        Integer       serial       Bead serial number.
17 - 18        String        eleType      DNA Element type
27 - 30        String        chainID      Chain identifier
32 - 39        Integer       eleSeq       Position of the element in a chain
41 - 48        Real(8.3)     x            Orthogonal coordinates for X
50 - 57        Real(8.3)     y            Orthogonal coordinates for Y
59 - 66        Real(8.3)     z            Orthogonal coordinates for Z
90 - 97        Real(8.3)     varDist      Variance of the observed spatial distribution

Details

• The serial number would be a number higher than the last record, CHROM, TER or DNAELE.
• DNA Element type brings a two-letter identifier for DNAELE, TF, for a transcription factor, CH for cohesin protein complex, for example.
• DNA elements must be considered as a separate chain, with its own chain identifier.
• The unit for coordinates is specified in LENGTH record.
• The variance of the observed spatial distribution is specially important in the case of experimental data. For data generated by simulations, this field can the set as 1.00.
• TER record must only appear when the chain have CHROM records. For a chain with DNAELE, TER should not be added.

Examples

         1         2         3         4         5         6         7         8         9        10
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
MODEL         1
CHROM         1 B3        C1          1  370.891  366.965  369.383          1      50000    1.000
CHROM         2 B3        C1          2  370.929  367.777  369.942      50001     100000    1.000
CHROM         3 B3        C1          3  370.836  368.751  369.875     100001     150000    1.000
CHROM         4 B3        C1          4  371.239  369.019  369.061     150001     200000    1.000
CHROM         5 B3        C1          5  371.711  368.817  368.213     200001     250000    1.000
TER           7 B3        C1  
DNAELE        8 TF        E1          1  370.546  368.831  369.345                          1.000

         1         2         3         4         5         6         7         8         9        10
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
CHROM        64 UN        C21        64 1306.813 1297.500   23.429   19890000   19920000    1.000
CHROM        65 UN        C21        65 1298.734 1297.474   17.162   19920000   19950000    1.000
TER          66 UN        C21
DNAELE       67 TF        EL1         1 1289.524 1297.727   17.935                          1.000
DNAELE       68 CH        EL2         1 1289.018 1306.404   18.680                          1.000