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GeneZilla specifications

Information


Unique identifier OMICS_07772
Name GeneZilla
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License Artistic License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Bill Majoros <>

Publications for GeneZilla

GeneZilla citations

 (19)
library_books

Draft Genome Sequence and Annotation of the Apicomplexan Parasite Besnoitia besnoiti

2017
PMCID: 5690326
PMID: 29146849
DOI: 10.1128/genomeA.01200-17

[…] that aligned with at least 70% coverage and 60% identity were independently aligned to the genome with genewise (). in addition, we ran two gene prediction tools previously trained for t. gondii, genezilla (), and two configurations of augustus () using or not using genewise alignments as evidence. prediction of the final gene set was carried out with evidence modeler software () […]

library_books

Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

2016
PMCID: 5182062
PMID: 27892853
DOI: 10.7554/eLife.19090.045

[…] while the other set was used to evaluate gene finder performance. based on our previous experience with annotation of oligohymenophoran ciliate genomes (, ; ), we focused on the gene finders genezilla (, ) (rrid:scr_014657) and augustus () (rrid:scr_008417). parameters were iteratively modified by automated implementation of algorithmic scripts to optimize sensitivity and specificity […]

library_books

Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites

2014
PMCID: 3901762
PMID: 24438588
DOI: 10.1186/1471-2164-15-42

[…] scaffolds. by comparing the databases, we obtained the number of protein distributions., four ab initio gene prediction programs were run on the genome: snap [], augustus [], glimmerhmm [], and genezilla [] with the model trained using the published mosquito gene information (a. gambiae, ae. aegypti and c. quinquefasciatus)., to estimate the accuracy of gene prediction, we undertook […]

library_books

Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila

2013
PMCID: 3608545
PMID: 23555191
DOI: 10.1371/journal.pbio.1001518

[…] different mating types. the strategy was developed as part of an ongoing reannotation of the t. thermophila macronuclear and micronuclear genomes. the gene-finding algorithms augustus and genezilla were re-trained for t. thermophila using a set of full-length rna-seq transcripts and used to perform gene predictions. additionally, we ran the aat tool against a jcvi in-house […]

library_books

Evaluating High Throughput Ab Initio Gene Finders to Discover Proteins Encoded in Eukaryotic Pathogen Genomes Missed by Laboratory Techniques

2012
PMCID: 3511556
PMID: 23226328
DOI: 10.1371/journal.pone.0050609

[…] model or functionality to create one for the target pathogen., four ab initio gene finder programs fulfilled the selection criteria–genemark.hmm , augustus , , snap , and glimmerhmm , . the programs genezilla , mgene (uses machine learning techniques), and conrad (based on conditional random fields) were tested but not included for evaluation due to consistent undocumented program crashes. […]

library_books

Comparative genomic analysis and phylogenetic position of Theileria equi

2012
PMCID: 3505731
PMID: 23137308
DOI: 10.1186/1471-2164-13-603

[…] were generated and assembled into 2355 contigs using pasa []., genes encoding trna’s were identified using trna scan-se []. gene models were predicted using the ab initio gene finding programs genezilla, glimmerhmm [], phat [] and snap [] that used 395 partial and full length high confidence genes in the training set. the training data was manually constructed and inspected […]


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GeneZilla institution(s)
Bioinformatics Department, The Institute for Genomic Research, Chinakville, MD, USA

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