Information Technology Reference
In-Depth Information
Entrez. If the CDD staff cannot find the Accession numbers for the sequences in the
records from the source databases, they locate appropriate sequences using BLAST.
Particular attention is paid to any resulting match that is linked to a structure record in
MMDB, and the staff substitute alignment rows with such sequences whenever possible.
Figure 3: VAST Structure Neighbors page.
The
top portion
of the page contains identifying information
about the 3D Domain, along with three functional bars. (
a
) The View bar. This bar allows a user to view a
selected alignment either as a graphic using Cn3D or as a sequence alignment in HTML, text, or mFASTA
format. The user may select which chains to display in the alignment by checking the boxes that appear to
the
left
of each neighbor in the
lower portion
of the page. (
b
) The nr-PDB bar. This bar allows a user to
either display all matching records in MMDB or to limit the displayed domains to only representatives of
the selected nr-PDB set. The user may also select how the matching domains are sorted in the display and
whether the results are shown as graphics or as tabulated data. (
c
) The Find bar. This bar allows the user to
find specific structural neighbors by entering their PDB or MMDB identifiers. (
d
) The
lower portion
of the
page displays a graphical alignment of the various matching domains. The
upper three bars
show summary
information about the query sequence: the
top bar
shows the maximum extent of alignment found on all the
sequences displayed on the current page (users should note that the appearance of this bar, therefore,
depends on which hits are displayed); the
middle bar
represents the query sequence itself that served as
input for the VAST search; and the
lower bar
shows any matching CDs and is identical to the CD bar on
the Structure Summary page. Listed below these three summary bars are the hits from the VAST search,
sorted according to the selection in the nr-PDB bar. The bars represent aligned regions, with gaps indicating
unaligned regions. To the
left
of each domain accession is a check box that can be used to select any
combination of domains to be displayed either on this page or using Cn3D. Moreover, each of the bars in
the display is itself a link, and placing the mouse pointer over any bar reveals both the extent of the
alignment by residue number and the data linked to the bar.
