Calculating RIP mutation in fungal genomes using RIPCAL
Repeat-induced point mutation (RIP) occurs in some fungal taxa, preferentially mutating C:G nucleotide pairs that reside within repetitive DNA and converting them to T:A. Within the taxon Pezizomycotina, RIP is biased towards mutation of CpA dinucleotides. RIP is an important feature of fungal genom...
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| Format: | Book Chapter |
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Springer
2015
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| Online Access: | http://hdl.handle.net/20.500.11937/42312 |
| _version_ | 1848756385386332160 |
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| author | Hane, James |
| author2 | M. van den Berg |
| author_facet | M. van den Berg Hane, James |
| author_sort | Hane, James |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Repeat-induced point mutation (RIP) occurs in some fungal taxa, preferentially mutating C:G nucleotide pairs that reside within repetitive DNA and converting them to T:A. Within the taxon Pezizomycotina, RIP is biased towards mutation of CpA dinucleotides. RIP is an important feature of fungal genomes as its distribution and extent have important implications for genome evolution. Early studies of RIP did not have access to vast amounts of genome sequence information; therefore RIP was measured within one or a handful of repeat sequences using ratios of dinucleotide frequencies. However as whole-genome sequences became available for fungi, it became possible to predict the repeat content of a whole genome and calculate RIP mutation across a large number of sequences from multiple repeat families. The software tool RIPCAL was developed for this purpose and since its release has become widely used in fungal genome analysis pipelines. |
| first_indexed | 2025-11-14T09:11:21Z |
| format | Book Chapter |
| id | curtin-20.500.11937-42312 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T09:11:21Z |
| publishDate | 2015 |
| publisher | Springer |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-423122023-02-27T07:34:28Z Calculating RIP mutation in fungal genomes using RIPCAL Hane, James M. van den Berg K. Maruthachalam Repeat-induced point mutation (RIP) Neurospora crassa Fungal genome analysis RIPCAL Repetitive DNA Genome evolution Repeat-induced point mutation (RIP) occurs in some fungal taxa, preferentially mutating C:G nucleotide pairs that reside within repetitive DNA and converting them to T:A. Within the taxon Pezizomycotina, RIP is biased towards mutation of CpA dinucleotides. RIP is an important feature of fungal genomes as its distribution and extent have important implications for genome evolution. Early studies of RIP did not have access to vast amounts of genome sequence information; therefore RIP was measured within one or a handful of repeat sequences using ratios of dinucleotide frequencies. However as whole-genome sequences became available for fungi, it became possible to predict the repeat content of a whole genome and calculate RIP mutation across a large number of sequences from multiple repeat families. The software tool RIPCAL was developed for this purpose and since its release has become widely used in fungal genome analysis pipelines. 2015 Book Chapter http://hdl.handle.net/20.500.11937/42312 Springer restricted |
| spellingShingle | Repeat-induced point mutation (RIP) Neurospora crassa Fungal genome analysis RIPCAL Repetitive DNA Genome evolution Hane, James Calculating RIP mutation in fungal genomes using RIPCAL |
| title | Calculating RIP mutation in fungal genomes using RIPCAL |
| title_full | Calculating RIP mutation in fungal genomes using RIPCAL |
| title_fullStr | Calculating RIP mutation in fungal genomes using RIPCAL |
| title_full_unstemmed | Calculating RIP mutation in fungal genomes using RIPCAL |
| title_short | Calculating RIP mutation in fungal genomes using RIPCAL |
| title_sort | calculating rip mutation in fungal genomes using ripcal |
| topic | Repeat-induced point mutation (RIP) Neurospora crassa Fungal genome analysis RIPCAL Repetitive DNA Genome evolution |
| url | http://hdl.handle.net/20.500.11937/42312 |