Home page of Tchourbanov Alexander

Recent presentations

• Presentation in Temple,TX
• First lecture in splicing
• Second lecture in splicing
• ROCKY '06 presentation
• Con Te Partiro

Project setup relating Ka/Ks to fidelity of phylogenetic reconstruction

• Java project setup files with batch scripts.

Available programs

• Homology-based gene structural prediction evaluation framework
  This Linux application has been used for comparative performance evaluation of EXALIN, EST2GENOME, GrailEXP, Spidey, BLAT, GIGOgene and Sim4 applications. Requires JVM of version 1.5 or higher to be installed on your machine.
• Ab initio gene structural prediction evaluation framework
  This online Java application uses different data sets to query the following ab initio gene structural prediction tools for the purposes of ROC curve reconstruction: CRAIG with the following ROC curves, Augustus with the following ROC curves, ExonScan, GeneSplicer, Genio, GenScan, HMMgene 1.1, NetGene2, NetUTR 1.0, NNSplice, SpliceView, SpliceScan, MZEF, geneID 1.2, Eukaryotic GeneMark.hmm, SpliceMachine, Bayesian SS sensor, Maximum Entropy SS sensor, MDD sensor, Markov chain SS sensor and Weight Matrix SS sensor. The application requires JVM version 1.5 or higher.
• Bayesian sensor (see description below)
• SpliceScan engine (see description below)
• MHMMotif program
  It uses mixture of Hidden Markov Models to detect clusters of sequential patterns
• GIGOgene 1.3 program (see description below)

Bayesian sensor

SpliceScan

My GIGOgene homology-based gene annotation tool

• Online implementation of GIGOgene engine
• GIGOgene 1.3 Installation instructions and Spliced Alignment program itself
• GIGOgene 1.0 CSB03 conference article
• GIGOGene 1.0 poster and latex poster files

Exon level precision based on Genie learning set of 462 human genes. Our GIGOgene application outperforms contemporary Homology Based annotation tools we have looked at in terms of exon level Sensitivity and Specificity. TE AE PE ESn ESp Galahad 4744 4909 4790 96.64% 99.04% Spidey 4827 4909 4847 98.33% 99.59% EST2Genome 4742 4909 4752 96.60% 99.79% Sim4 4837 4909 4845 98.53% 99.83% BLAT 4832 4909 4902 98.43% 98.57% GIGOgene 4864 4909 4865 99.08% 99.98% We have compared performance of different programs on human genes containing microexons. First we parsed gene structures for the whole human genome to find genes containing microexons (2-11nt). Then we carefully examined splice sites to be canononical in the genomic structures predicted. We compared predicted structures with other program annotations and got the following results in terms of exonic level Sensitivity and Specificity: TE AE PE ESn ESp Galahad 1220 1422 1278 85.79% 95.46% Spidey 1251 1422 1334 87.97% 93.78% EST2Genome 1270 1422 1318 89.31% 96.36% Sim4 1278 1422 1326 89.87% 96.38% BLAT 1375 1422 1424 96.69% 96.56% GIGOgene 1420 1422 1422 99.86% 99.86%

• Test files available from here

Here I am going to keep certain useful links and other useful information.