XdomView is a chime-based visualization tool that maps the domain boundaries of the input PDB chain, obtained from protein structure classification databases (CATH,
SCOP, NCBI,
3DEE and
DALI) to its tertiary
structure. It also runs BLAST2 for the input PDB chain sequence against all protein sequences in the ExInt* database and maps the intron positions
and phases of aligned search results on the input protein's 3D structure.
XdomView is a useful visualization tool for scientists working on gene and
protein evolution and structural modeling and classification.
Input
parameters:
-
PDB
code
Standard four letter code
beginning with a number and followed by three alpha-numeric
characters.
- ChainID
(optional)
If the structure for the chosen PDB code has multiple
chains, it is necessary to specify the chain identifier (a
single alpha-numeric character). If chain identifiers are not
specified, then the program automatically selects the
alphabetically lowest chain as default for visualization.
- BLAST
e-value cut-off (Default
:1e-10)
This e-value [integers, float or scientific notation]
specifies the cut-off for performing BLAST2 against ExInt
database to select homologous proteins for the input PDB chain
sequence.
* ExInt -
Repository of intron positions, phase and protein sequences of
all multi-exonic eukaryotic genes available in GenBank 122. http://intron.bic.nus.edu.sg/exint/exint.html
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