SubVis
Scott Barlowe, Heather Coan, and Robert Youker
2017-01-06
About
Description
Other Project Pages
Known Issues
Included Data
Getting Started
Options Tab
VIZ Tab: Overview
VIZ Tab: Detail
VIZ Tab: Search
Error Messages
Notes
References
About:
Subvis version 2.0.0
Scott Barlowe, Heather Coan, and Robert Youker
Western Carolina University
Uses: R (>= 3.3.0), JavaScript
Licensing: GNU General Purpose License
Description:
Software tool for visual analysis of substitution matrix
effects on pairwise protein sequence alignment. Utilizes
Shiny for interface components, R for alignment processing,
and JavaScript for visualization.
Other Project Pages:
1. https://github.com/sabarlowe/SubVis
Included Data:
Location: (extdata/Example_custom_matrix and
extdata/Example_FASTA_files)
1. Four protein sequences in FASTA format
(gpr12.fasta, gpr6.fasta)
(Human.fasta, Xenla.fasta)
(fNucl.fasta, pFalc.fasta)
2. A custom matrix developed by Rios et al. (gpcrtm.txt)
A scaled and scaled adjusted matrix reported by
Yu and Altschul (scaled_BLSM.txt, scaled_adj_BLSM.txt)
The DISORDER matrix proposed by Radivojac et al.
(disorder.txt)
3. BLOSUM62 matrix used for varying penalties (BLS.txt)
4. Three custom master files (masterFile_gpcrtm.txt,
masterFile_scaled_adj_bls.txt, and falcNuc.txt) listing
the file names of custom matrices and their associated
gap and extension costs
Getting Started:
(Requires availability of a web browser):
1. Install R version >= 3.3.0
2. Install required R packages (and any dependencies):
'shiny'
'Biostrings'
3. Install and load SubVis package
4. Launch the SubVis at the RStudio prompt with
'> SubVis::startSubVis()'
NOTE: ENTERING SEQUENCE TEXT (INSTEAD OF FILE UPLOAD)
AND USING CUSTOM MATRICES REQUIRES READ/WRITE
PERMISSIONS IN THE SUBVIS INSTALLATION DIRECTORY
Main tabs: Options, Viz, and Help:
After launching, there are three tabs: Options, Viz, and
Help
Options tab: Loading data, matrices, and parameters:
The Options tab includes the following:
1. Protein sequences (one per file) must be in FASTA
format. There are two example FASTA files in the
test folder.
2. Sequences can be loaded by either entering the text
(including by copy/pasting) or by file selection.
In the case of text entry, text files with the fasta
sequences are created in the extdata/Example_FASTA_files
directory located in the SubVis install directory.
These files can be saved for future use.
NOTE: ENTERING SEQUENCE TEXT (INSTEAD OF FILE UPLOAD)
REQUIRES READ/WRITE PERMISSIONS IN THE SUBVIS
INSTALLATION DIRECTORY
3. An error message will be generated if
a. Either textbox or file selection is empty
b. Spaces are in the sequences
c. The header and sequences of both are identical
d. The sequences are identical
2. BLOSUM and PAM matrices can be selected by checking
the appropriate box. Gaps and extension costs can be
changed with the associated text boxes.
An error message will be generated if
a. The gap entry is empty or is not a number.
b. The extension entry is empty or is not a number,
3. A custom matrix in the form of the
predefined matrices can be loaded from
a text file. The basic form is
First row --> Characters representing lookup
table.
First col --> Transpose of first row starting
at row 2
All other entries (intersection of amino acids)
are substitution values
A B C D E F . . .
A
B
C
D
E
F
...
Custom matrices are loaded by selecting a master file.
This file lists the names of the files that contain
the custom matrices. Both files should be located in
extdata/Example_custom_matrix located in the SubVis
installation directory. The format is:
custom_matrix_name0 gap_cost0 extension_cost0
custom_matrix_name1 gap_cost1 extension_cost1
custom_matrix_name2 gap_cost2 extension_cost2
...and so on...
Spaces separate the custom matrix name, gap cost, and
extension cost for each matrix. EACH LINE MUST END
WITH A NEWLINE CHARACTER TO AVOID ERRORS/WARNINGS.
THIS INCLUDES THE LAST LINE LISTING A CUSTOM MATRIX.
In the display, the custom matrix is labeled "CM"
followed by the order in which they are listed in the
custom matrix master file (For example, CM0, CM1, etc.)
An error message will be generated if
a. The custom matrix radio box is set to "ON" and the
file selection is empty
b. The format of the custom matrix is not acceptable
NOTE: USING CUSTOM MATRICES REQUIRES READ/WRITE
PERMISSIONS IN THE SUBVIS INSTALLATION DIRECTORY
4. The score type can be selected by text boxes and a drop-down
menu
5. After all parameters are entered, clicking the "GO" button
located under the "PERFORM ALIGNMENT" label will changed
the view to the Overview visualization
Note: Each time a change in the options tab is made,
the GO button (in the Overview or detail view)
must be clicked
Viz tab: Overview, Detail view, and Search:
There are three options that can be selected with a drop-down
box: Overview, Detail view, and Search
Overview:
Each row (except the last) represents a percent identity
type. Within each row, the pid for the selected matrices
are sorted. The last row is the sorted overall score.
All PID colors are normalized together. The score colors
are normalized separate from the PIDs. A legend in the
bottom left shows the color scheme along with the minimum
and maximum values for the PID and score.
Interaction: Mouse move
1. When the mouse moves over a matrix type, the
corresponding matrix in the other rows are identified.
At the same time, the corresponding detail information
(matrix type, percent identity, and score) are shown
in the bottom right.
Interaction: Size
1. '+' enlarges the display and '-' shrinks the
display
Detail View:
Score is located under the matrix type for each alignment
pair along the left side. Amino acids are represented by
a color-coded box.
Interaction: Size
1. '+' enlarges the display
2. '-' shrinks the display
Interaction: Mouse over an amino acid
1. Histogram showing the number of each amino acid in that
column
2. Log-odds score (or any substitution value entered
into a custom matrix) and the amino acid substitution
displayed under the score for each alignment
3. Amino acid, log-odds score (or any substitution value
entered into a custom matrix), and the amino acid
subsitution is shown in the top right
4. The gap and extension costs for the selected amino acid
(under the mouse) is shown in the top left
Interaction: Classification
1. Classify amino acids according to [1] and whether an
amino acid substitution is conserved (log-odds > 0)
or not (log-odds < 0). Conservation classification
may not apply depending on substitution value entered
into custom matrix.
Interaction: Amino Acid Representation
1. 'Alpha On/Off' - Show amino acid instead of boxes
Interaction: Nagivation
1. 'S' - Go to position 1
2. 'E' - Go to the end of the alignment with the maximum
length
3. 'U' - Scroll up if all matrix types will not fit onto
display space
4. 'D' - Scroll down if all matrix types will not fit
onto display space
5. '<' - Go backward in the alignment
6. '>' - Go forward in the alignment
7. 'Pair' - Show both the pattern and subject for each matrix
type
8. 'Patt' - Show only the pattern for each matrix type
9. 'Subj' - Show only the subject for each matrix type
Search:
Interaction: POS (Requires clicking 'GO')
1. Go to a position by entering column in text box
(Requires clicking 'Go')
Interaction: Search (All require clicking 'Go')
1. 'NONE' - No search function on (default)
2. 'INDEL' - Shows the insertions and deletions in red
3. 'MATCH' - Shows the positions that match in both the
pattern and subject
4. 'SEQ' - The amino acid to be searched for
Error Messages:
Error messages are generated in the following scenarios
under on the top left of the VIZ tab
1. 'ERROR: No Sequence Text':
Generated if either sequence text box is empty
2. 'ERROR: No Sequence File':
Generated if either sequence file selection is
empty
3. 'ERROR: Identical Pattern and Subject:
Generated if the two sequence inputs (header
information and sequences) are identical
4. 'ERROR: Identical Sequences':
Generated if the two sequences inputs (sequences
only) are the same
5. 'ERROR: Non-Custom Gap':
Bad gap value for the BLOSUM/PAM matrices
provided (empty value or not a number)
6. 'ERROR: Non-Custom Ext':
Bad extension value for the BLOSUM/PAM matrices
provided (empty value or not a number)
7. 'ERROR: Bad Sequence or Matrix':
Error in Biostring's pairwiseAlignment function.
Could indicate, among other possibilities, a
poorly constructed sequence not indicated by
another error message or a poorly constructed
custom matrix.
8. 'ERROR: No Custom Matrix Selected':
Custom matrix turned on without selecting a custom
matrix master file
9. 'ERROR: Custom Gap':
Bad gap cost for the custom matrix read from the
custom matrix file (not a number)
10. 'ERROR: Custom Ext':
Bad extension cost for the custom matrix read from the
custom matrix file (not a number)
Notes:
1. Log-odds score (or any substitution value entered
into a custom matrix) for pairs involving a gap are
reported as undefined
References:
1. Pages, H., Aboyoun, P., Gentleman, R., DebRoy, S.:
Biostrings: String Objects Representing Biological
Sequences, and Matching Algorithms. R package version
2.32.0
2. Pearson, W.R., Lipman, D.J.: Improved tools for
biological sequence comparison. Proc. Natl. Acad. Sci.
USA 85(8), 2444{2448 (1988)
3. Pommie, C., Levadoux, S., Sabatier, R., Lefranc, G.,
Lefranc, M.: Imgt standardized criteria for statistical
analysis of immunoglobulin v-region amino acid
properties. Journal of Molecular Recognition 17(1),
(2004)
4. R Core Team: R: A Language and Environment for
Statistical Computing. R Foundation for Statistical
Computing, Vienna, Austria (2013). R Foundation for
Statistical Computing. http://www.R-project.org/
5. RStudio, Inc.: Shiny: Web Application Framework for R.
(2014). R package version 0.10.1.
http://CRAN.R-project.org/package=shiny
6. Rios, S., Fernandez, M.F., Caltabiano, G., Campillo,
M., Pardo, L., Gonzalez, A.: Gpcrtm: An amino acid
substitution matrix for the transmembrane region of
class a g protein-coupled receptors. BMC Bioinformatics
16(206). (2015)
7. Yu, Y., Altschul, S.F.: The construction of amino
acid substitution matrices for the comparison of proteins
with non-standard compositions. Bioinformatics 21(7):
902-911. (2004)
8. Radivojac, P., Obradovic, Z., Brown, C.J., Dunker, A.K.:
Improving sequence alignments for intrinsically disordered
proteins. Pacific Symposium on Biocomputing 7:589-600.
(2002)