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Protocols

ParsEval specifications

Information


Unique identifier OMICS_14476
Name ParsEval
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A genomic sequence
Input format GFF3
Operating system Unix/Linux, Mac OS
Programming languages C
License ISC License
Computer skills Advanced
Stability Stable
Maintained No

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Publication for ParsEval

ParsEval citations

 (5)
library_books

Consideration of non canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz 1 genome sequence

2017
BMC Res Notes
PMCID: 5716242
PMID: 29202864
DOI: 10.1186/s13104-017-2985-y

[…] Calculation of gene prediction statistics as well as comparison to the Col-0 annotation via identification of RBHs was carried out by custom Python scripts as previously described []. ParsEval [] was applied to compare the GeneSet_Nd1_v1.0 and GeneSet_Nd1_v1.1 in more detail. […]

call_split

PacBio assembly of a Plasmodium knowlesi genome sequence with Hi C correction and manual annotation of the SICAvar gene family

2017
PMCID: 5798397
PMID: 28720171
DOI: 10.1017/S0031182017001329
call_split See protocol

[…] on was selected, and the AUGUSTUS score threshold was set to 0·5.To evaluate the gene models produced by the MAKER2 and Companion approaches, a comparison between both annotations was performed using ParsEval (Standage and Brendel, ). The unique genes identified by each approach were selected for manual curation using Artemis (Rutherford et al. ). To assign functional annotation to the predicted p […]

library_books

Seqping: gene prediction pipeline for plant genomes using self training gene models and transcriptomic data

2017
BMC Bioinformatics
PMCID: 5333190
DOI: 10.1186/s12859-016-1426-6

[…] to accurately identify gene structure. The predicted rice genes from Seqping were also independently verified using a different approach. Comparison of the Seqping models to the MSU annotation using ParsEval [] yielded 87.70% shared gene loci. These results indicate that Seqping had the best prediction for the rice genome. […]

library_books

Proteogenomics produces comprehensive and highly accurate protein coding gene annotation in a complete genome assembly of Malassezia sympodialis

2017
Nucleic Acids Res
PMCID: 5389616
PMID: 28100699
DOI: 10.1093/nar/gkx006

[…] The previously published annotation () was transferred to our new genome assembly using the liftOver program () and then compared to our current annotation using ParsEval (). A chain file for liftOver was constructed by aligning the old and new genome assemblies with BLAT and processing the alignments according to the instructions on the UCSC Genome Browser wi […]

library_books

The neurotranscriptome of the Aedes aegypti mosquito

2016
BMC Genomics
PMCID: 4704297
PMID: 26738925
DOI: 10.1186/s12864-015-2239-0

[…] include the top 10) are listed in Additional file . To determine the proportion of transcripts that were updated as compared to the VectorBase annotations (Fig. ; AaegL2.1 and AaegL3.3), we used the parseval tool in the AEGeAn package to compare gff3 annotation files [].We note that due to the evolving nature of annotations in Ae. aegypti and the fact that our orthology relies only on a single sp […]

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ParsEval institution(s)
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA; Department of Biology, Indiana University, Bloomington, IN, USA; School of Informatics and Computing, Indiana University, Bloomington, IN, USA
ParsEval funding source(s)
This work was supported in part by the U.S.A. National Science Foundation Plant Genome Research Program grant ISO#1126267.

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