Selecting a cluster from your search results generates the following
view
**PLEASE NOTE THE FOLLOWING PICTURE PROVIDES AN EXAMPLE OF AN OUTPUT FOR ONE OF OUR SISTER DATABASES
LUMBRIBASE.
THE INFORMATION IS RELEVANT TO TARDIBASE THOUGH THE NAMES OF THE CLUSTERS ARE HDC NOT LRC***
- Cluster Summary:
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
- Library info.
Gives the names of libraries used, the stage (currently only mixed) and the number of
contigs from each.
- BLAST info
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.
- Contig info.
The red header bar on the second section has the contig number and length of
the consensus sequence for this contig.
- Protein translation link
The blue header bar on the second section has a link to the
predicted protein
translation of the contig.
- List of sequences
This is a list of ESTs (coloured by type - see above) which make up this
particular contig. Click on the EST name to retreive the genbank entry.
- Contig view
Under the list of sequence ID's 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).
- Trace view link
Is a link to the DNA sequence chromatograms (traces) of the ESTs which is
the ultimate reference source for any queries about that particular sequencing
reaction.
- Consensus Sequence
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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