STINGpaint:
WWW tool for sequence and MULTIPLE sequence alignment coloring
STINGpaint
STINGpaint was developed to allow the presentation of residue characteristics in the Sequence Frame.
As a consequence, during development of STING project,
we have slightly expanded on STINGpaint idea and adopted it for use
with Multiple Sequence Alignment (MSA) coloring. It turns out that this tool
was very interesting for people wanting to easily grasp specifically colored regions
along the MSA. In addition, our STINGpaint is also a part of our ongoing
work for STING-2, a package that will be able to show both sequnce alignmnts
(in the Sequence Frame) and structures (in the Graphics Frame)
for respective sequences!
STINGpaint now supports following sequence and MSA formats:
- Coloring sequence of any PDB entry
- Coloring any sequence presented to STINGpaint in FASTA format
- Coloring MSA in PRISM (An-Suei Yang) output format
PRISM is a sequence/structure /threading/homology modeling program
developed byAn-Suei Yang in the Honig laboratory
- Coloring MSA in PSI-BLAST output format
- Coloring MSA in GCG output format
For test purposes, a user can access sample formats
(given for each option at STINGpaint)
and just copy_and_paste them
into the working area of STINGpaint. It is our experience that
analysis of MSA can be greatly enhanced using STINGpaint!
Note: We strongly suggest that user tries:
Using STINGpaint with different background color
and experiment with the size of the MSA to be STINGpainted!
It is our experience that only CPU with 400MHz have
acceptable speed for large MSA files, intended for STINGpaint with
background color option! However, results might be very informative
for the MSA analysis! Related to this issue,
see work by
W.R. Taylor (Protein Eng 1997 Jul;10(7):743-746;
"Residual colours: a proposal for aminochromography").
Sequence color coding
Residues are color coded with respect to Hydrophobicity and
charged groups!
Residues: AVLIMFP are colored gray! [small & hydrophobic]
Residues: STYNQWG are colored green [polar]
Residues: D E are colored red! [negatively charged]
Residues: R K are colored blue! [positively charged]
Residues: C is colored yellow! [disulfide bridge forming]
STINGpaint output sample:
1 50
WRP25 SGPWSWCDPA TGYQVSALTG CRAMVKLQCV KSQVPEAVLR DCCQQLADIN
WRP26 SGPWMWCDPA TGYQVSALTG CRAMVKLQCV GSQVPEAVLR DCCQQLADIN
WRP24 SGPWMWCYPG QAFQVPALPA CRPLLRLQCN GCQVPEAVLR DCCQQLAHIS
WRP27 SGPWMWCDPA MGHRVRPLMG CRAMVKLQCV GNQVPEAIQR DCCQELANIT
AI1FAT ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
AI2FAT ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
51 100
WRP25 NEWCRCGDLS SMLRSVYQEL GVREGKVLPG CRKEVMKLTA ASVPEVCKVP
WRP26 NEWCRCGDLS SSLRSVYQEL GVREGKVLPG CRKEVMKLTA ASVPEVCKVP
WRP24 NEWCRCG~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
WRP27 NNWCRCHDLG SMLNSVYQEL GAREGTVFPG CRKEVMKLTV ASVPAVCKVP
AI1FAT ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~
AI2FAT ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~