Lesson
7 - Intervals on the Map - Syntenic relationships
Tools and Techniques
In this last lesson on interval data we will discuss contigs and syntenic
relationships between species. We'll look at the multimap display and briefly
touch on the ACEDB native query syntax.
ACEDB query language
The ACEDB software (the database software unlying
and managing all these genome databases) has its own query syntax. Since
it requires you to have a fairly good understanding of the organization
and links between items in the database, it is most appropriate when you
can clearly express what you are looking for and you are very familiar
with the database structure. It is the most complete and powerful search
form, but also the most complex. The biggest advantage of the ACEDB query
language is that you can restrict your search based on values from other
classes, for example, finding all the probes for loci that are associated
with QTLs; the restriction is put on the Locus class (associated with QTL),
but what is returned to you are Probe records.
To use an ACEDB query, you must know the correct
syntax, class and field names. You will have access to the data model,
but there is no fill-in-the-blank, or drop-down lists to help you. A powerful
feature of the syntax is the FOLLOW keyword, which lets you follow links
between classes involved in your query. In the example above, we would
start with the Locus class, restrict it to those associated with QTLs,
then FOLLOW those loci to their corresponding Probe records. ACEDB queries
will return all records matching your criteria. The query is case insensitive,
but the logical operators (AND, OR, NOT, etc.) must be in uppercase.
Example 7.1 - The example below will take you
through constructing and executing some ACEDB queries. This should give
you a good feeling for the syntax and how to form simple and complex queries.
In addition, there are a number of excellent
documents describing the ACEDB query syntax available from the ACEDB
documentation library - if you find this search method useful, these
will provide you with more examples and instructions.
RiceGenes
If you have a RiceGenes Database comment or question contact AngelaBaldo,
Curator.
Syntenic relationships
As more is learned about the content and organization
of the genomes of various organisms, scientists are learning that "blocks"
of genes are often preserved in some fashion across species. In other words,
a segment of chromosome 3 in corn may have the same genes, in the same
order, as a segment of chromosome 7 in rice; this tutorial will refer to
these regions as homoeologous segments. Certainly, the more closely related
the species are, the more likely it is that we can detect homoeologous
segments. Much of the currently available information is based on a fairly
gross scale (the "blocks" may be many, many cM big) and we are still learning
more about how well these relationships hold up at a finer scale.
Knowing where these homoeologous segments are can
help you leverage the information available from a well-studied organism,
or extrapolate information from one species to another. For example, if
you know where an important gene is located in maize, you might be able
to predict where its counterpart is located in oat. Because it is unlikely
that all organisms will receive the same resources dedicated to model organisms,
it is very important to build informational bridges like this. The
cereal crops (corn, wheat, oat, rice, barley, etc.) are all closely related.
Of these, rice has the smallest genome, and is often used as the "model"
cereal. The RiceGenes database has quite a bit of information on how genomic
segments from several grass species are related, and may be a good resource
for looking at syntenic relationships among the grasses. 7.2 - The databases
below have examples that illustrate where to find and how to interpret
information about homoeologous segments. Investigate as many as you like!
RiceGenes
If you have a RiceGenes Database comment or question contact Marci
Blinstrub, Curator.
GrainGenes
If you have a GrainGenes Database comment or question contact Gerry
Lazo, Curator.
Multimap displays
Another way to look at the similarity and alignment
of maps (chromosomes) from the same species or maps from different species
is with the Multimap display. This is another one of the special graphical
displays available with the ACEDB software. Multimap lets you line up several
maps and draws lines between loci that are in common between adjacent maps.
It determines which loci are the "same" based on the locus name or some
other field that the curator has defined for this purpose. To see what
the Multimap display looks like, check out the example below.
Example 7.3 - The databases below have examples
that illustrate where to find and how to interpret information about Multimaps.
The ones with the stars were designed as part of the tutorial; others were
supplied by the database curators. Investigate as many as you like!
SolGenes
If you have a SolGenes Database comment or question contact Sam
Beer, Curator.
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