ALEXA_gg_42_2 (CHICKEN): Detailed statistics and comments
The following page provides detailed statistics, comments and figures describing the ALEXA_gg_42_2 pre-computed microarray design
Species: Gallus gallus
Design Summary and Custom UCSC Tracks
To view details on the probes for a specific gene of interest, download the annotation file for this design. This file contains links to custom UCSC tracks for every gene (the gene name is also a link). A link to an example gene is also provided below.
Figures describing the genome used to create the ALEXA_gg_42_2 design
Note: Additional statistics and figures pertaining to the input genome for this design can be downloaded seperately.
Basic summary of EnsEMBL gene models used for this design
Note that most genes currently have only a single transcript annotated
Distribution of transcript lengths
Transcripts are divided into two bins. Those shorter than 10,000 bp in length and those greater than 10,000
Distribution of exon lengths
Exons are divided into two bins. Those shorter than 500 bp in length and those greater than 500
Figures describing the ALEXA_gg_42_2 design itself (Probe stats - After Filtering)
Note: The following statistics pertain to all probe types combined (Exon, Intron, Exon-Junction, Exon-Boundary and Random Negative-Control probes) but are limited to only those probes that pass the filtering step. Similar statistics corresponding to all probes before filtering were used to determine suitable thresholds for the filtering step.
Each of the plots shown below as well as many others are available for each probe type individually and can be downloaded as a complete package. This package also includes statistics for the complete set of unfiltered probes.
The length of probes is allowed to vary by +/- 10 bp to achieve the target Tm
Probe Melting Temperature
'Probe Tm' values are calcuated by a Nearest Neighbor method and reported in degrees Celsius
Probe Folding Energy
'Folding energy' values are the minimum free energy values calculated by PairFold for each probe sequence and reported in kcal/mol
Number of Probes Per Gene
The number of probes extracted for a particular gene is dependent on the number of known exons for that gene. As the number of exons increases, the number of exon and exon-boundary probes increases in a linear fashion and the number of exon-junction probes increases in a factorial fashion (n!/[[n-2]!2!] where n is the number of exons).
Probe Specificity - Length of Non-Specific Hits
'EnsEMBL Non-specific Hit Length' values are the largest BLAST hit observed between a probe sequence and an EnsEMBL transcript from a locus other than the one targeted by the probe (i.e. a closely related sequence from another gene)
Probe coverage - A measure of the success of probe design for each gene
Each gene has an ideal number of probes based on the number of exons in that gene. 'Probe coverage' values are calculated for each gene and represent the ratio of successful probes designed compared to the ideal number possible for a gene with n exons. In some rare cases, single exons are divided into multiple sections (occurs when the boundaries of an exon are ambiguous). This can lead to a probe coverage value of greater than 100%. Note that the success of probe design varies dramatically between genes. However, 59.0% of genes in this design have a probe coverage of 75% or greater. The stringency of filtering can be reduced to increase this percentage.