:: DESCRIPTION
xGDBvm is a web-based platform for annotating and visualizing eukaryotic genomes.
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Duvick J, Standage DS, Merchant N, Brendel VP.
xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud.
Plant Cell. 2016 Apr;28(4):840-54. doi: 10.1105/tpc.15.00933. Epub 2016 Mar 28. PMID: 27020957; PMCID: PMC4863385.
:: DESCRIPTION
BWASP/R is a complete workflow that allows efficient, scalable and entirely reproducible analyses of raw DNA methylation sequencing data.
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Morandin C, Brendel VP.
Tools and applications for integrative analysis of DNA methylation in social insects.
Mol Ecol Resour. 2021 Dec 3. doi: 10.1111/1755-0998.13566. Epub ahead of print. PMID: 34861105.
:: DESCRIPTION
OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Li Li, Christian J. Stoeckert, Jr., and David S. Roos
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Genome Res. 2003 13: 2178-2189
:: DESCRIPTION
Serial Cloner has been developed to provide a light molecular biology software to both Macintosh and Windows users. Serial Cloner reads and write DNA Strider-compatible files and import and export files in the universal FASTA format. Serial Cloner also import files saved in the Vector NTI, ApE, pDRAW32 and GenBank formats. Import from MacVector is also possible now. Powerful graphical display tools and simple interfaces help the analysis and construction steps in a very intuitive way. Serial Cloner handles Annotations and Features both in the sequence and in the Graphic Map.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
IMMpractical implements various Markov chain model-based methods for analysis of DNA sequences.Markov chain models are commonly used for content-based appraisal of coding potential in genomic DNA.
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sparks, M.E., Brendel, V. and Dorman, K.S. (2007)
Markov model variants for appraisal of coding potential in plant DNA.
LNBI. 4463:394-405.
:: DESCRIPTION
MuSeqBox (Multi-query Sequence Blast Output Examination)is a program designed for multi-query sequence BLAST output examination. It examines the BLAST output, extracts the informative parameters of BLAST hits, and saves them in tabular form in either text or HTML format. The hit tables are optionally further analyzed with the program to produce subsets of BLAST hits according to user-specified criteria. In particular, BLASTX output may be further analyzed to indicate queries that might potentially be alternatively spliced transcripts (e.g., an extra large segment of insertion or deletion), full-length coding sequences, or contains repeat structures.
::DEVELOPER
The Brendel Group @ Indiana University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Xing, L. and Brendel, V. (2000)
MuSeqBox: a program for multi-query sequence BLAST output examination.
Bioinformatics 17, 744-745.
:: 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.
::DEVELOPER
The Brendel Group @ Indiana University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Standage, D.S. & Brendel, V.P. (2011)
ParsEval: parallel comparison and analysis of gene structure annotations
BMC Bioinformatics 2012, 13:187
:: DESCRIPTION
MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the k-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5′-complete coverage.
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sparks, M.E. & Brendel, V. (2008)
MetWAMer: eukaryotic translation initiation site prediction.
BMC Bioinformatics, 9, 381.
:: DESCRIPTION
yrGATE (Your Gene structure Annotation Tool for Eukaryotes) is a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes.yrGATE provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the acceptance of annotations into published gene sets. yrGATE is designed to facilitate rapid and accurate annotation of emerging genomes as well as to confirm, refine, or correct currently published annotations. yrGATE is highly portable and supports different standard input and output formats.
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
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.
:: DESCRIPTION
BSSM4GSQ generate training data and parameterizations for Bayesian splice site models (as used in the GeneSeqer package).
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
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.
