What's New

Fresh off the press:

Morandin, C., Brendel, V.P., Sundström, L.; Helanterä, H. & Mikheyev, A. (2019) Changes in gene DNA methylation and expression networks accompany caste specialization and age-related physiological changes in a social insect methylation. Molecular Ecology, 28, 1975-1993. [PubMed ID: 30809873] [online article] [PDF]

The future of computational genomics:

  Brendel, V.P. (2018) From small RNA discoveries to a new paradigm in computational genomics? New Phytol. 220, 659-660. [PubMed ID: 30324739] [online article] [PDF]

  Check out our new bgRAMOSE Jetstream image!


TSRchitect is now available as a Bioconductor R package!

Brendel group in the Indiana Daily Student news (Dec. 12, 2016)

Volker Brendel elected AAAS Fellow (Oct. 2016); IU News Release (Nov. 21, 2016)

Check out our github site!


The Brendel Group provides domain expertise to advise the Jetstream national science and engineering cloud project.

V. Brendel serves on the CyVerse External Advisory Board.

V. Brendel serves as Consulting Editor of The Plant Cell.

PlantGDB News:

xGDBvm on YouTube


What does our "Bioinformatics2go" page offer? (1) Bioinformatics programs served over the web. Follow the links to access the program interfaces for analyzing your data via web servers or services. (2) Bioinformatics software available for downloading for local installation. Follow the instructions on the "Download" links.

Gene structure prediction tools


Description: A spliced alignment tool. Citation: Brendel, V., Xing, L. & Zhu, W. (2004) Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 20, 1157-1169. [PubMed ID: 14764557] [PDF] Web Implementations: GeneSeqer @ USD GeneSeqer @ PlantGDB Web Services: Download: Download GeneSeqer


Description: Statistical splice site prediction. This program is distributed as part of the GeneSeqer package. Citation: Brendel, V., Xing, L. & Zhu, W. (2004) Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 20, 1157-1169. [PubMed ID: 14764557] [PDF] Web Implementations: SplicePredictor @ USD Web Services: Download: Download GeneSeqer


Description: Software to generate training data and parameterizations for Bayesian splice site models (as used in the GeneSeqer package). Citation: Sparks, M.E. & Brendel, V. (2005) Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants. Bioinformatics 21, iii20-iii30. [PubMed ID: 16306388] [PDF] Web Implementations: n/a Download: Download BSSM4GSQ


Description: A gene structure annotation tool. Citation: Wilkerson, M.D., Schlueter, S.D. & Brendel, V. (2006) yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. Genome Biol. 7, R58. [PubMed ID: 16859520] [PDF] Web Implementations: yrGATE @ PlantGDB Download: Download yrGATE


Description: ASpipe is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments. Citation: Wang, B.-B., O'Toole, M., Brendel, V. & Young, N.D. (2008) Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes. BMC Plant Biol. 8:17. [PubMed ID: 18282305] [online article] Web Implementations: ASIP @ PlantGDB is a web site displaying alternative splicing events derived from ASpipe applications to plant genomes. Download: Download ASpipe from


Description: MetWAMer currently implements five distinct methods for translation initiation site (TIS) identification. Citation: Sparks, M.E. & Brendel, V. (2008) MetWAMer: eukaryotic translation initiation site prediction. BMC Bioinformatics, 9, 381. [abstract] [PDF] Web Implementations: n/a Download: Download MetWAMER code and test data


Description: IMMpractical implements various Markov chain model-based methods for analysis of DNA sequences. Citation: Sparks, M.E., Brendel, V. & Dorman, K.S. (2007) Markov model variants for appraisal of coding potential in plant DNA. In I. Mandoiu & A. Zelikovsky (eds.), 2007 International Symposium on Bioinformatics Research and Applications, May 7-10, 2007, Georgia State University, Atlanta GA, U.S.A.. Lecture Notes in Bioinformatics 4463, 394-405. [online article] [conference proceedings] Web Implementations: n/a Download: Download IMMpractical from

Genome browsing tools


Description: The xGDB project provides scientists with an online portal for the integration of diverse sources of genomic data. Portals allow researchers to effectively target a specific scientific question by customizing their interactions with available data. Citation: Schlueter S.D., Wilkerson M.D., Dong Q., & Brendel V. (2006) xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features. Genome Biol. 7(11): R111. [PubMed ID: 17116260] [abstract] [PDF] Web Implementations: xGDB @ PlantGDB Download: Download xGDB from


Description: A pretty old Java-based visualization tool for GeneSeqer output. Citation: Zhu, W. & Brendel, V. (2002) Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions. Bioinformatics 18, 761-762. [PubMed ID: 12050073] [online abstract] [PDF] [cited in PMC] Download: Download MyGV

Genome assembly tools


Description: A contig assembly tool. Citation: Dong, Q., Wilkerson, M.D. & Brendel, V. (2007) Tracembler - software for in silico chromosome walking in unassembled genomes. BMC Bioinformatics 8, 151. [PubMed ID: 17490482] [online abstract] [PDF] Web Implementations: Tracembler Download: Download Tracembler

Protein analysis tools


Description: SAPS stands for Statistical Analysis of Protein Sequences, and SSPA is an acronym for Significant Segment Pair Alignment. These programs are rather old (see citations), but still in use. I am making the old code available as is for now, hoping for some time soon to update the code. In the meantime, give me feedback and suggestions! Volker Brendel, December 16, 2008. Citations: SAPS - Brendel, V., Bucher, P., Nourbakhsh, I.R., Blaisdell, B.E. & Karlin, S. (1992) Methods and algorithms for statistical analysis of protein sequences. Proc. Natl. Acad. Sci. USA 89, 2002-2006. [PubMed ID: 1549558] [PDF]; SSPA - Karlin, S., Weinstock, G. & Brendel, V. (1995) Bacterial classifications derived from RecA protein sequence comparisons. J. Bacteriol. 177, 6881-6893. [PubMed ID: 7592482] Web Implementations: SAPS @ EBI; SAPS @ Mobyle Download: Download SAPS-SSPA



Description: ParsEval is a program for comparing two sets of gene structure annotations (provided as GFF3 files) for the same genomic region. Comparison statistics are calculated for each genic region, as well as for the entire region overall. If the user has installed GenomeTools, then ParsEval can also create graphical output showing the genomic context of the two sets of annotations. Citation:Standage, D.S. & Brendel, V.P. (2012) ParsEval: parallel comparison and analysis of gene structure annotations. BMC Bioinformatics 13, 187. [PubMed ID: 22852583] [online abstract] [PDF] Download: Download ParsEval


Description: MuSeqBox is a program to parse BLAST output and store attributes of BLAST hits in tabular form. The user can apply a number of selection criteria to filter out hits with particular attributes. MuSeqBox provides a powerful annotation tool for large sets of query sequences that are simultaneously compared against a database with any of the standard stand-alone or network–client BLAST programs. Citation: Xing, L. & Brendel, V. (2001) Multi-query sequence BLAST output examination with MuSeqBox. Bioinformatics 17, 744-745. [PubMed ID: 11524378] [PDF] Web Implementations: MuSeqBox @ PlantGDB Download: Download MuSeqBox


Description: mRNAmarkup is a tool still in development. Not quite ready for distribution, but coming soon! (stable code version available below, requiring more documentation) Citation: Tourigny, J. & Brendel, V.P. (2021) mRNAmarkup. To be submitted. Download: Download mRNAmarkup


Description: The PairwiseStatSig program estimates the pairwise statistical significance of a pairwise local alignment of two protein sequences independent of any database using censored Maximum Likelihood Fitting. Citation: Agrawal, A., Brendel, V. & Huang, X. (2008) Pairwise statistical significance versus database statistical significance for local alignment of protein sequences. In I.I. Măndoiu, R. Sunderraman & A.Z. Zelikovsky (eds.), 2008 International Symposium on Bioinformatics Research and Applications, May 6-9, 2008, Georgia State University, Atlanta GA, U.S.A.. Lecture Notes in Bioinformatics 4983, 50-61. [online abstract]; Agrawal, A., Brendel, V. & Huang, X. (2008) Pairwise statistical significance and empirical determination of effective gap opening penalties for protein local sequence alignment. Int. J. of Computational Biol. and Drug Design, 1(4), 347-367 Download: Download PairwiseStatSig