What is on the Barley1 GeneChip?
In general, probe sets on the Barley1 GeneChip are composed of 11 pairs
of 25-mer oligonucleotide derived principally from the last 600 bases of
each exemplar consensus sequence or singleton sequences. The
term "probe" refers to the fixed nucleic acid molecules used
to interrogate the experimental samples, while "target"
refers to the experimental sample (i.e., the labeled RNA). Each probe
pair contains a perfect match oligonucleotide
and a mismatch control containing a single substitution at the 13th base.
Technical notes on GeneChip arrays and their operation can be found at
the Affymetrix website.
Oligonucleotide placement within each represented exemplar sequence
can be viewed online
from PLEXdb, or on Windows computers using
information for the Barley1 array is hosted on the
NetAffx Analysis Center at Affymetrix
Search and Access Probe Sets on Barley1:
Sequence Similarity-Based Search
There are two major options, either
through courtesy of the
databases, or locally
Option 1. Search for Barley1 GeneChip content with user's
PLEXdb BLAST page for Barley1 and Arabidopsis
ATH1-121501 GeneChip Exemplar
Dedicated BLAST page for Barley GeneChip Exemplar
Dedicated VMATCH page to search against Barley1
GeneChip probes. This tool match your sequences against
Barley GeneChip probes. The result tells you if there is a
match and where the match occurs. It is useful for
biologists to find out if there are available oligo probes for
Option 2. Searches starting with Barley1 GeneChip exemplar
- Find microarray oligo probe (set)
for a known Barley1 contig:
displays details of the exemplar sequence, its member ESTs and
alignments, and its oligo probes..
- Align Barley1 exemplar sequences with other cereal genes and
genomes on the Gramene Rice Genome Browser
for cross-species comparison.