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Protocols

RIPCAL specifications

Information


Unique identifier OMICS_22803
Name RIPCAL
Interface Command line interface, Graphical user interface, Application programming interface
Restrictions to use Academic or non-commercial use
Input data A sequence input or a pre-aligned sequence or a repeat coordinate input.
Input format FASTA,FASTA+GFF,CLUSTALW
Operating system Unix/Linux, Windows
Programming languages Perl
License Free License
Computer skills Advanced
Version 1.0.4
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline James Hane
  • person_outline Richard Oliver

Publication for RIPCAL

RIPCAL citations

 (28)
library_books

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici repentis reveals chromosomal variations and genome plasticity

2018
BMC Genomics
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] ator, LTRHarvest (GenomeTools) v1.5.1 (minimum distance 200 bp and maximum distance 5000) and LTRDigest (GenomeTools) v1.5.1 [].De novo repeat families were searched for RIP-like SNP mutations [] via RIPCAL v2.0 [, ]. Repeat family mutation sites were plotted for the highest mutation rates CpA- > TpA per kb. Segmental duplication in M4 was determined based on Nucmer alignments greater than 90% ide […]

library_books

Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi

2018
Sci Rep
PMCID: 5897359
PMID: 29651164
DOI: 10.1038/s41598-018-24301-6

[…] chostomum and M. rhizophila genomes, respectively. Accordingly, many of these sequences may belong to TE superfamilies that did not meet the quantity or length requirements used to test for RIP using RIPCAL. Amongst the TEs identified across genomes, Class I members were found to consistently outnumber those in Class II. LTRs and TIRs were generally found to be the most prevalent Class I and Class […]

library_books

Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol specific phospholipase C genes (PI PLC)

2018
BMC Genomics
PMCID: 5773145
PMID: 29343217
DOI: 10.1186/s12864-018-4440-4

[…] than 400 bp in length and at least 80% identical), were aligned using clustalX []. This alignment was used for automated analysis of RIP in C. cacaofunesta TEs and for estimating dinucleotides using RIPCAL (http://www.sourceforge.net/projects/ripcal) []. RIPCAL output provides the numbers of transitions (Ti), transversions (Tv), and dinucleotide targets used in all possible transitions for each T […]

library_books

Reference Assembly and Annotation of the Pyrenophora teres f. teres Isolate 0 1

2017
PMCID: 5765338
PMID: 29167271
DOI: 10.1534/g3.117.300196

[…] ns, as well as average gene densities within each region. OcculterCut was run with the updated 0-1 genome input as a FASTA file, the updated 0-1 annotation in GFF3 format, and default run parameters. RIPCAL () was implemented to scan for evidence of repeat-induced point mutations (RIP) within the repetitive content of the 0-1 genome. Repeat family sequences of >400 bp of the five most common repea […]

library_books

Genome sequence of the ectophytic fungus Ramichloridium luteum reveals unique evolutionary adaptations to plant surface niche

2017
BMC Genomics
PMCID: 5602860
PMID: 28915794
DOI: 10.1186/s12864-017-4118-3

[…] y rRNAmmer v. 1.2 (http://www.cbs.dtu.dk/services/RNAmmer), tRNAscan-SE v. 1.3.1 [] and Rfam (http://rfam.xfam.org). For calculation of RIP indices, dinucleotide frequencies were determined using the RIPCAL program []. […]

call_split

Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

2017
BMC Genomics
PMCID: 5576322
PMID: 28851275
DOI: 10.1186/s12864-017-4083-x
call_split See protocol

[…] wise manner with REPET tools (refalign, refalign2fasta) to derive a multiple alignment, (ii) TE copies smaller than 400 bp and with less than 80 % identity with the consensus were filtered out, (iii) RIPCAL [] was applied to each TE family, using the copy with highest GC content to compute base transition, and (iv) in-house Perl and R scripts were used to calculate dinucleotide bias and produce gr […]

Citations

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RIPCAL institution(s)
Australian Centre for Necrotrophic Fungal Pathogens, Faculty of Health Sciences, Murdoch University, Murdoch, WA, Australia
RIPCAL funding source(s)
Supported by a PHD scholarship provided by the Grains Research & Development Corporation (Barton, ACT, 2600, Australia).

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