Bioinformatics2go
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
GeneSeqer
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] Download: Download GeneSeqer
SplicePredictor
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] Download: Download GeneSeqer
BSSM4GSQ
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] Download: Download BSSM4GSQ
yrGATE
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] Download: Download yrGATE
ASpipe
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] Download: Download ASpipe from sourceforge.net
MetWAMer
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
IMMpractical
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. [abstract] Web Implementations: n/a Download: Download IMMpractical from sourceforge.net
Genome browsing tools
xGDB
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] [online article] [PDF] Web Implementations: xGDBvm Project Download: Download xGDB from sourceforge.net
MyGV
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
Tracembler
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] Download: Download Tracembler
Protein analysis tools
SAPS, SSPA
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
Utilities
ParsEval
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
MuSeqBox
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] Download: Download MuSeqBox
mRNAmarkup
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: Brendel, V.P., et al. (2024) mRNAmarkup. To be submitted. Download: Download mRNAmarkup
PairwiseStatSig
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