Selecting a cluster from your search results generates the following
view
- TOP LEFT
A brief summary of the cluster
indicating its index number, the number and types of sequences belonging
to the cluster, the number of contigs predicted for the cluster by the assembly
program (usually cap3 is used to generate cluster assembly's, however when
cap3 fails, phrap is used)and the libraries represented by the cluster. For
sequence types :
- Blue = EST
- Red = cDNA
- Magenta = genomic DNA
- Green = GSS
- TOP RIGHT
To the right of the summary table is the precomputed
blast information available on the cluster. By moving the mouse over the
appropriate button, different hits will be displayed within the text
window (NB This only works for some browsers e..g Netscape 6). Clicking
on the buttons launches a new window showing the BLAST output. It should
be noted that similarity scores > e^-99 are scored as 0,
"no significant hits
" indicates that no hits with a similarity score of < e^-5 were obtained
and 'no hits' indicate that no blast hits were
found for this cluster.
- MIDDLE
Below the header information is data pertaining
to each contig - the contig number, length of the sequence, number of ESTs
which make up this particular contig and a list of these ESTs (coloured by
type - see above). Click on the EST name to retreive the genbank entry.
- BOTTOM
Under the contig information is a simple graphic indicating the position
of the sequences relative to the contig. The sequences are coloured
according to quality/alignment information. Gold indicates sequence of
high quality; purple indicates lower quality sequence used in creating
the consensus sequence. Genbank entries can again be
retreived by clicking on each sequence within the graphic. You can also view
the alignment used for assembly of the cluster by clicking on the consensus
(red box). Finally, below
the graphic the cluster consensus sequence is given. The Blast button
below this takes you to our in-house BLAST server automatically pasting
in the consensus sequence
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