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This
option displays Milestone Unigene Member consensus sequences, to which
all EST members are aligned. A user can select from two options.
Option
1: All milestone sorghum clusters
All Milestone Clusters are available in a list box. Those beginning with
a zero (0_*) are singletons. Those beginning with a one (1_*) are what
Phrap identifies as contigs of one, effectively singletons that have some
substantial similarity to contigs of two or more members. Those beginning
with a two (2_*) are contigs of two or more members.
Upon selecting a contig to view, one is presented with a split screen
(the width of either side is adjustable). The left-hand side identifies
the individual ESTs belonging to the cluster. Discrepancies between an
individual member and the consensus sequence are highlighted by a grey
background.
Option
2: All milestone sorghum clusters which contain SSRs SNPs
The first step is to establish query parameters. In the first list box
one can select either 'All contigs' or a specific SSR-containing contig.
If all contigs are selected, then it might be useful, but is not necessary,
to define the selection further.
The second list box lets a user select contigs of any genotype or a user
can select only those contigs that include an EST from a given genotype
(A002 = S. bicolor, BTx623; A001 = S. halepense; A003 = S. propinquum).
The next three list boxes allow a user to view SNPs if desired.
The ranks are from 1 through 9, with 1 having the greatest probability
of being a true SNP, 9 the lowest.
The following list box defines whether a microsatellite must differ from
a selected genotype.
The next two permit a user to define the quality of SSRs to be displayed,
while the those following define the length range of the SSR.
Two final options permit one to search for a specific microsatellite motif
(e.g., cgg) and/or motif length.
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