RAFTS3 protocols

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RAFTS3 specifications

Information


Unique identifier OMICS_12068
Name RAFTS3
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Beta
Requirements
MATLAB Compiler Runtime
Maintained Yes

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Maintainer


  • person_outline Ricardo Assunção Vialle <>

Publication for RAFTS3

RAFTS3 in pipelines

 (3)
2017
PMCID: 5313630
PMID: 28209838
DOI: 10.1128/genomeA.01666-16

[…] was determined using bowtie2 (). gene prediction was performed using genemarkes version 4.29 (). annotation of the protein coding genes was based on best-hit searches against the nr database using rafts3 () and interproscan (). aragorn version 1.2.36 () was used for trna gene identification., a total of 7,445,102 paired-end reads were obtained for f. multimorphosa cbs 980.96t genome […]

2016
PMCID: 4966464
PMID: 27469960
DOI: 10.1128/genomeA.00731-16

[…] with fgap software (). protein-coding genes were predicted with genemark-es (). annotation for 11,984 predicted genes were assigned based on similarity searches against the nr database using rafts3 () and interproscan () comparisons. the genome contained 37 trnas identified using aragorn ()., the information generated via this genome sequence might provide better understanding […]

2016
PMCID: 4974309
PMID: 27491988
DOI: 10.1128/genomeA.00735-16

[…] were predicted with genemark-es (). gap closure was performed with fgap software (). annotation for 11,681 predicted genes were assigned based on similarity searches against the nr database using rafts3 () and interproscan () comparisons. the genome contained 36 trnas identified using aragorn ()., information about the genome sequence of this black yeast might provide a better understanding […]

RAFTS3 in publications

 (3)
PMCID: 5640708
PMID: 29062304
DOI: 10.3389/fmicb.2017.01924

[…] and salzberg, ) and the mapped reads assembled with spades v3.6.2 (bankevich et al., )., protein-coding genes were predicted with genemark-es v4.39 (besemer, ). the automatic annotation was done by rafts3 (vialle et al., ) best hits comparison with self-score cutoff of 0.5 using a black yeast protein database available on (www.broadinstitute.org/annotation/genome/black_yeasts/). protein domain […]

PMCID: 4974309
PMID: 27491988
DOI: 10.1128/genomeA.00735-16

[…] were predicted with genemark-es (). gap closure was performed with fgap software (). annotation for 11,681 predicted genes were assigned based on similarity searches against the nr database using rafts3 () and interproscan () comparisons. the genome contained 36 trnas identified using aragorn ()., information about the genome sequence of this black yeast might provide a better understanding […]

PMCID: 4966464
PMID: 27469960
DOI: 10.1128/genomeA.00731-16

[…] with fgap software (). protein-coding genes were predicted with genemark-es (). annotation for 11,984 predicted genes were assigned based on similarity searches against the nr database using rafts3 () and interproscan () comparisons. the genome contained 37 trnas identified using aragorn ()., the information generated via this genome sequence might provide better understanding […]

RAFTS3 institution(s)
Laboratory of Bioinformatics, Sector of Professional and Technological Education, Federal University of Paraná, Curitiba, Paraná, Brazil; Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
RAFTS3 funding source(s)
National Institute of Science and Technologies of Biological Nitrogen Fixation, Fundação Araucária, CAPES and CNPq

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