Bioinformatics2go

What's New

Group:

Jon Duvick interviewed by HPCwire!

Recent publications:

Rauch, H.B., Patrick, T.L., Klusman, K.M., Battistuzzi, F.U., Mei, W,. Brendel, V.P. & Lal, S.K. (2013) Discovery and Expression Analysis of Alternative Splicing Events Conserved among Plant SR Proteins. Mol. Biol. Evol.,doi: 10.1093/molbev/mst238 First published online: December 19, 2013. [PubMed ID: 24356560] [online article (corrected proof)] [PDF (Advance Access)]

Yi, G., Brendel, V.P., Shu, C., Li, P., Palanathan, S. & Kao, C.C. (2013) Single Nucleotide Polymorphisms of Human STING Can Affect Innate Immune Response to Cyclic Dinucleotides. PLoS One 8, e77846. [PubMed ID: 24204993] [online article] [PDF]

PlantGDB News:

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]

Web Implementations: GeneSeqer @ USD GeneSeqer @ PlantGDB
Web Services:

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]

Web Implementations: SplicePredictor @ USD
Web Services:

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]

Web Implementations: n/a

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]

Web Implementations: yrGATE @ PlantGDB

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]

Web Implementations: ASIP @ PlantGDB is a web site displaying alternative splicing events derived from ASpipe applications to plant genomes.

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. [online article] [conference proceedings]

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] [abstract] [PDF]

Web Implementations: xGDB @ PlantGDB

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]

Web Implementations: Tracembler

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]

Web Implementations: MuSeqBox @ PlantGDB

Download: Download MuSeqBox

mRNAmarkup



Description: mRNAmarkup is a tool still in development. Not quite ready for distribution, but coming soon! (4-18-2013 promise)

Citation: Brendel, V.P. (2013) mRNAmarkup.To be submitted.

Web Implementations:

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