NimbleGen selects 5 optimal probes for each of the 2325 predicted coding sequences of Clostridium novyi-NT using a proprietary probe screening system developed exclusively for the MAS platform. Probe sets are selected which uniquely represent the genomic target or gene transcripts of interest, and which are predicted to have excellent hybridization characteristics. Our predictive software is based on a combination of NimbleGen's innovative Tm-balanced probe selection coupled with heuristic and AI predictive methods derived from a growing volume of experimental data. NimbleGen manufactures custom, high-density DNA arrays based on its proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system.
This a unique, composite key consisting of the DESIGN_ID, ROW_NUM and COL_NUM.
DESIGN_NOTE
A comment field suitable for placing information necessary for data analysis, for instance if you want to analyze sets of probes and/or genes together that don’t separate out using SELECTION_CRITERIA, CONTAINER, PROBE_CLASS or other information.
SELECTION_CRITERIA
For most standard designs, this field will contain some information about how the probe was selected for inclusion on the array.
SEQ_ID
The NimbleGen sequence identifier. Used to group the probe pairs together to generate average difference values. A SEQ_ID is a 17 character string that looks like:
SEQUENCE
The DNA sequence synthesized on the array
MISMATCH
The number of mismatches in the PROBE_SEQUENCE. Generally 0 (for the perfect match probe) or 2 (for the corresponding mismatch probe).
MATCH_INDEX
Integer number that ties probe pairs together. Using the combination of MATCH_INDEX and MISMATCH you can retrieve and distinguish the members of the probe pair. Many controls have a MATCH_INDEX of ‘0’ since they are not paired with a mismatch probe.
FEATURE_ID
A unique number used to tie together multiple features that compose a larger entity called a feature cell. For 4:9 format, the four individual features that comprise the larger feature cell will all have the same FEATURE_ID
ROW_NUM
The Y coordinate of the feature within the CONTAINER holding the feature.
COL_NUM
The X coordinate of the feature within the CONTAINER holding the feature.
POSITION
When populated, this contains the position of the probe within the parent sequence
DESIGN_ID
This is the NimbleGen identifier for the design.
X
The absolute X coordinate of the feature on the array
Y
The absolute Y coordinate of the feature on the array
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