HJEM


Poster
with graphics


DeltaProt: Molecular comparison of proteins based on sequence alignments.
(© University of Tromsø 2005, version 1.1 Jan 2007.)

A Matlab© companion Toolbox.

Steinar Thorvaldsen1, Tor Flå1 and Nils P. Willassen1,2
1University of Tromsø and 2Norwegian Structural Biology Centre
9037 Tromsø - Norway.

Download Matlab code of the DeltaProt Toolbox  here!
This software can be used freely for academic, non-profit purposes.
Note: Matlab Statistical Toolbox is used in some functions.

Abstract. In bioinformatics there is an increasing desire for more statistical methods in the data analysis. We present statistical methods and trend-tests that are useful when the protein sequences in alignments can be divided into two or more populations based on known features or traits such as preference of temperature, pH, salt concentration or pressure. The algorithms are considered valuable for discovering differences between populations at a molecular level, and the approach has been successfully applied in the research on extremophile organisms. The toolbox also contains procedures for comparative plots of alignments and substitution matrices.
 

Edited by: Steinar Thorvaldsen
Latest update: January 16, 2007.

 

File name Brief description

manual.pdf

Program's user guide.
DeltaProt.m
DeltaProt1.m		 Main program scripts

readfasta.m
aa2int.m
dssp2int.m
wasa2int.m

Reads text files (alignments) in fasta format. Transforms symbols of amino acids.
Convert secondary structure to numbers.
Convert 3D predictions to numbers.
findSeqSimilarity.m
findSeqSiteVar.m		 Finds overall similarity between input seq.
Finds variations and conserved sites(Var=1).

aaCount.m
aaFreq.m
aaFreqPlot.m
aa2bin.m
aaDeltaFreq.m
aaDeltaFreqPlot.m
aaAnova2Pvalues.m

Calculates counts, frequences and compositional changes in sequences extracted previously from file, and plots results.

substPairsCount.m
substPairsPvalues.m
substMHPvalues.m
substPairs2aa.m
substPairs2bin.m
FisherExtest.m*
chi2Test.m*
MantelHaenTest.m*
substPairsPlot.m
substCountSort.m
substPvalueSort

 Calculates substitutions, insertions and
deletions between aligned sequence pairs. Run the appropriate statistical test (Fisher's exact with mid-P, chi-square, or stratified Mantel-Haenszel) and present the results.

filterAlignedseq.m
propAnovaPvalues.m
propNormalityTest.m*
propPairedPvalues.m
propKendallPvalues.m
cumKendallTest.m*
FDR.m

Reduces sequence data to property data.
Runs one-way ANOVA test.
Data-adaptive goodness of fit to normality.
Runs paired trend-tests (t-test or Wilcoxon).
Runs a monotonic trend-test.
cumulative Mann-Kendall test.
Multiple test correction by False Discovery Rate

aa_prop60.xls

Excel-file with the physicochemical properties.

align_vibrio.tgz

Zipped file with Python scripts.
This script will not run on another computer without some work and adjustments of the code

* Implemented statistical test


References
S. Thorvaldsen, T. Flå and N. P. Willassen: Extracting molecular diversity between populations through sequence alignments. Lecture Notes in Bioinformatics, Vol. 3745, Springer-Verlag 2005, pp. 317-328.

S. Thorvaldsen, E. Ytterstad and T. Flå: Property-dependent analysis of aligned proteins from two or more populations. Proceedings of the 4th Asia-Pacific Bioinformatics Conference (Eds.: T. Jiang et al.). Imperial College Press 2006, pp. 169-178.

DeltaProt is accepted for software demo at CompLife06 and ECCB06.