A High Density (HD) search, also known as a zoom-in search, retrieves
CGH or ChIP probes that span specific regions of the genome of a given
species. For a general discussion of HD Search, see What
is a High Density (HD) search.
eArray provides several different search methods to retrieve HD probes
from the eArray HD probe database, based on the way that you specify the
regions of the genome to be searched. Click one of the links below for
instructions on how to do a specific type of search.
Parameter |
Instructions/Details |
Job Information |
Search Name |
Type a name that will help
you later identify the results from this search. |
Species |
Select the desired species
from the list. Information about the applicable current genome build appears
in Build Number. |
Probe Options |
Filters |
Select one of the options
below. If relevant, a field appears in which you can type a filter value.
Click
for a description of how HD search applies filters.
None
– The program does not
apply any of the filters in the list.
Average Spacing – Type
a number of base pairs in the field that appears. This defines the average
number of base pairs between the centers of the retrieved probes in each
genomic interval. See .
Probes Per
Interval – Type
a number of probes in the field that appears. This defines the maximum
number of probes that HD Search retrieves for each genomic interval. See
.
Total Probes
– Type a number of probes
in the field that appears. This defines the total number of probes HD
Search collectively returns for all specified genomic intervals. See .
Guidance from Agilent on probe density for CGH microarrays |
Prefer Catalog Probes |
(Available for HD-CGH probe
searches) To give preference to Agilent catalog probes in the probe selection
process, mark this check box. If two probes are close to each other for
a given probe interval, HD search selects the Agilent Catalog probe. |
Use TM Filter |
For HD-ChIP searches, select
YES or NO.
For HD-CGH Searches, the program always applies this filter for genomic
intervals searches.
Most probes in the Agilent
HD database have been Tm-matched. However, probes that do not pass the
Agilent Tm filters are also available. These probes lie in regions in
which no optimal-Tm probes exist. To access these probes, select NO in Use
TM Filter. Select YES (the
default) if you only want Tm-matched probes. |
Similarity Filter
|
Optimally, Agilent HD probes
will hybridize to one, and only one genomic location. However, sequence
redundancy is observed within most target genomes. To enable you to investigate
non-unique regions, eArray provides probes that hybridize to more than
one genomic location.
Three options with varying
levels of similarity stringencies are provided to select the appropriate
subset of probes. The availability of these options varies by species
and by application type.
No
Filter – The
program does not apply a similarity filter, and no probes in the queried
region are filtered out based on sequence similarity. With this option,
the Use Non-Unique Probe Filter
option becomes available, which you can use to select an upper limit of
probe perfect matches to the genome.
Perfect
Match Filter –
Filters out all probes that have 100% similarity to more than one genomic
location.
Similarity
Score Filter –
The most stringent filter. Filters out all probes with secondary genomic
alignments that could potentially impact probe performance.
Guidance
from Agilent on similarity filters for HD-CGH searches
|
Use Non-Unique Probe Filter |
(Available if you select
No Filter in Similarity Filter)
Non-unique probes map to more than one location in the target genome.
Mark this check box to remove these probes.
When you select this option,
Max Perfect Genomic Hits becomes
available. By default, this value is set to 1, which removes probes if
they map to more than one genomic location. However, you can set this
to a higher number. For example, if you type 3
in Max Perfect Genomic Hits, the filter only removes a probe if it maps
to four or more locations in the target genome. |
Interval Options |
Select HD Search by |
Keep this parameter set
to Genomic Intervals. |
Extended Interval Boundary
|
Type the number of 5' base
pairs and 3' base pairs by which you want to move out the start and end
points of all of your genomic intervals. This can help retrieve additional
probes that lie outside your initially defined regions.
For example, if you type
500 in 5'
base pairs and 300
in 3' base pairs, eArray extends an original interval of 9000–10000
to 8500–10300. |
Genomic Intervals |
(Required) Type either
a chromosomal location or a cytoband in the box. You can specify multiple
intervals separated by pipe "|" characters, but all of the intervals
must be of the same type. See Genomic
interval formats.
To upload a file of chromosomal
locations or cytobands, click Upload.
See Upload data for probe
searches. |
Include Regions
|
(Available for HD-CGH searches)
Select one of the options below. You can use this parameter to restrict
your HD-CGH probe search to only exonic, or only intragenic regions of
the genome.
All
– Retrieves probes in
all of the specified genomic region, both within
and outside of gene boundaries.
Exonic
– Retrieves probes in
exonic sequences within genes in the specified genomic region. When you
select this option, the Gene Confidence list appears. Select the appropriate
.
Intragenic
– Retrieves probes found
within gene boundaries, whether or not they are found in exonic sequences.
When you select this option, the Gene Confidence list appears. Select
the appropriate .
Additional
guidance from Agilent on how to target exons
|
Standard Exclusion Interval |
Agilent provides many sets
of standard exclusion intervals, based on annotation tracks. To ignore
the genomic regions that are defined in one or more of these sets, mark
this option, then select the desired set(s) from the list that appears.
Control-click the names of additional sets to select them. During an HD
search, exclusion intervals are ignored, and no probes are returned for
these regions. |
Custom Exclusion Interval |
To ignore the genomic intervals
defined in a file of genomic intervals, mark this option, then click Upload Interval File. See Upload
data for Probe Searches. During an HD search, exclusion intervals
are ignored, and no probes are returned for these regions. |
Parameter |
Instructions/Details |
Job Information |
Search Name |
(Required) Type a name
that will help you later identify the results from this search. |
Species |
(Required) Select the desired
species from the list. Information about the applicable current genome
build appears in Build Number. |
Prefer Catalog Probes |
(Available for HD-CGH probe
searches) To give preference to Agilent catalog probes in the probe selection
process, mark this check box. If two probes are close to each other for
a given probe interval, HD search selects the Agilent Catalog probe. |
Advanced Search Interval
|
(Required) Follow these
steps to upload your file of search interval settings:
Prepare
a file of intervals and settings. For details, see Upload
data for probe searches.
Click
Browse.
A Choose file dialog box appears.
Select
the desired search intervals file, then click Open.
This file must contain the required information for each desired interval
Click
Upload.
The Preview of Search Intervals pane appears. The pane lists the first
few rows from the file. To see a list of all of the imported rows, click
Show All.
If
the first row of your uploaded file contains column headings, mark My uploaded file contains column headings.
This prevents eArray from interpreting your column headings as actual
search interval information. eArray depends on the order of columns, not
column headings, to interpret the information in your uploaded file.
|
Interval Options |
Select HD Search by |
This parameter is set to
Genomic Intervals, and it cannot be changed. |
Extend Interval Boundary |
Type the number of 5' base
pairs and 3' base pairs by which you want to move out the start and end
points of all of your genomic intervals. This can help retrieve additional
probes that lie outside the initially defined regions of your genomic
intervals.
For example, if you type 500
in 5' base pairs and 300
for 3' base pairs, eArray extends an original interval of 9000–10000 to 8500–10300. |
Include Regions |
(Available for HD-CGH searches)
Select one of the options below. You can use this parameter to restrict
your HD-CGH probe search to only exonic, or only intragenic regions of
the genome.
All
– Retrieves probes in
all of the specified genomic region, both within
and outside of gene boundaries.
Exonic
– Retrieves probes in
exonic sequences within genes in the specified genomic region. When you
select this option, the Gene Confidence list appears. Select the appropriate
.
Intragenic
– Retrieves probes found
within gene boundaries, whether or not they are found in exonic sequences.
When you select this option, the Gene Confidence list appears. Select
the appropriate .
Additional
guidance from Agilent on how to target exons
|
Standard Exclusion Interval |
Agilent provides many sets
of standard exclusion intervals, based on annotation tracks. To ignore
the genomic regions that are defined in one or more of these sets, mark
this option, then select the desired set(s) from the list that appears.
Control-click the names of additional sets to select them. During an HD
search, exclusion intervals are ignored, and no probes are returned for
these regions. |
Custom Exclusion Interval |
To ignore the genomic intervals
defined in a file of genomic intervals, mark this option, then click Upload Interval File. See Upload
data for Probe Searches. During an HD search, exclusion intervals
are ignored, and no probes are returned for these regions. |
Before you begin, if you have many probes that you want to retrieve,
prepare a *.txt file that contains the desired probe IDs. See Upload
data for probe searches.
This search method is only available for HD-CGH probe searches.
Parameter |
Instructions/Details |
Job Information |
Search Name |
Type a name that will help
you later identify the results from this search. |
Species |
Select the desired species
from the list. Information about the applicable current genome build appears
in Build Number. |
Probe Options |
Filters |
Select one of the options
below. If relevant, a field appears in which you can type a filter value.
Click
for a description of how HD search applies filters.
None
– The program does not
apply any of the filters in the list.
Average Spacing – Type
a number of base pairs in the field that appears. This defines the average
number of base pairs between the centers of the retrieved probes in each
genomic interval. See .
Probes Per
Interval – Type
a number of probes in the field that appears. This defines the maximum
number of probes that HD Search retrieves for each genomic interval. See
.
Total Probes
– Type a number of probes
in the field that appears. This defines the total number of probes HD
Search collectively returns for all specified genomic intervals. See .
Guidance from Agilent on probe density for CGH microarrays |
Prefer Catalog Probes |
(Available for HD-CGH probe
searches) To give preference to Agilent catalog probes in the probe selection
process, mark this check box. If two probes are close to each other for
a given probe interval, HD search selects the Agilent Catalog probe. |
Use TM Filter |
For HD-ChIP searches, select
YES or NO.
For HD-CGH Searches, the program always applies this filter for genomic
intervals searches.
Most probes in the Agilent
HD database have been Tm-matched. However, probes that do not pass the
Agilent Tm filters are also available. These probes lie in regions in
which no optimal-Tm probes exist. To access these probes, select NO in Use
TM Filter. Select YES (the
default) if you only want Tm-matched probes. |
Similarity Filter
|
Optimally, Agilent HD probes
will hybridize to one, and only one genomic location. However, sequence
redundancy is observed within most target genomes. To enable you to investigate
non-unique regions, eArray provides probes that hybridize to more than
one genomic location.
Three options with varying
levels of similarity stringencies are provided to select the appropriate
subset of probes. The availability of these options varies by species
and by application type.
No
Filter – The
program does not apply a similarity filter, and no probes in the queried
region are filtered out based on sequence similarity. With this option,
the Use Non-Unique Probe Filter
option becomes available, which you can use to select an upper limit of
probe perfect matches to the genome.
Perfect
Match Filter –
Filters out all probes that have 100% similarity to more than one genomic
location.
Similarity
Score Filter –
The most stringent filter. Filters out all probes with secondary genomic
alignments that could potentially impact probe performance.
Guidance
from Agilent on similarity filters for HD-CGH searches
|
Use Non-Unique Probe Filter |
(Available if you select
No Filter in Similarity Filter)
Non-unique probes map to more than one location in the target genome.
Mark this check box to remove these probes.
When you select this option,
Max Perfect Genomic Hits becomes
available. By default, this value is set to 1, which removes probes if
they map to more than one genomic location. However, you can set this
to a higher number. For example, if you type 3
in Max Perfect Genomic Hits, the filter only removes a probe if it maps
to four or more locations in the target genome. |
Interval Options |
Select HD Search by |
Keep this parameter set
to Gene Annotations. |
Extended Interval Boundary
|
Type the number of 5' base
pairs and 3' base pairs by which you want to move out the start and end
points of all of your genomic intervals. This can help retrieve additional
probes that lie outside the initially defined regions of your genomic
intervals.
For example, if you type 500
in 5' base pairs and 300
for 3' base pairs, eArray extends an original interval of 9000–10000 to 8500–10300. |
Gene Annotations |
(Required) Type a gene
annotation such as a GenBank accession number (for example, NM_016660
or AY884282)
or a gene symbol (for example, H3N2
or CTSB)
in the box. Use pipe "|" characters to separate multiple annotations.
You can also upload a *.txt
file of gene annotations. For information on the required file format,
see Upload data for probe
searches. Follow these steps:
Click
Upload.
A file name window appears.
Click
Browse.
A file browser appears.
Select
the desired file, then click Open.
The location of the file appears in File Name.
Click
Upload File. eArray uploads the
gene annotations, and displays them in pipe-separated format in the HD
search pane.
eArray resolves annotations
to genomic intervals before it starts your search. |
Include Regions
|
(Available for HD-CGH searches)
Select one of the options below. You can use this parameter to restrict
your HD-CGH probe search to only exonic, or only intragenic regions of
the genome.
All
– Retrieves probes in
all of the specified genomic region, both within
and outside of gene boundaries.
Exonic
– Retrieves probes in
exonic sequences within genes in the specified genomic region. When you
select this option, the Gene Confidence list appears. Select the appropriate
.
Intragenic
– Retrieves probes found
within gene boundaries, whether or not they are found in exonic sequences.
When you select this option, the Gene Confidence list appears. Select
the appropriate .
Additional
guidance from Agilent on how to target exons
|
Standard Exclusion Interval |
Agilent provides many sets
of standard exclusion intervals, based on annotation tracks. To ignore
the genomic regions that are defined in one or more of these sets, mark
this option, then select the desired set(s) from the list that appears.
Control-click the names of additional sets to select them. During an HD
search, exclusion intervals are ignored, and no probes are returned for
these regions. |
Custom Exclusion Interval |
To ignore the genomic intervals
defined in a file of genomic intervals, mark this option, then click Upload Interval File. See Upload
data for Probe Searches. During an HD search, exclusion intervals
are ignored, and no probes are returned for these regions. |