/Recent content in Welcome to symcurve on symcurveHugo -- gohugo.ioenCopyright (c) 2020-2024 HyasThu, 07 Sep 2023 17:19:07 +0200/docs/guides/about/Thu, 07 Sep 2023 16:04:48 +0200/docs/guides/about/The SymCurve software gets its name from the notion of DNA having “symmetry of curvature”. The idea is to look for evidence of DNA intrinsically having symmetrical curvature/bendability properties at the points where it wraps a Eukaryotic nucleosome core particle./docs/guides/algorithm/Thu, 07 Sep 2023 16:04:48 +0200/docs/guides/algorithm/DNA step parameters The diagram below shows the six main ways that two consecutive base pairs are distanced from each other./docs/guides/example/Thu, 07 Sep 2023 16:04:48 +0200/docs/guides/example/Sequence Consider the 500 nucleotides of sequences below. It’s enough to wrap at least two eukaryotic nucleosomes. CCAACATTTTGACTTTTTGGGAGGGCACTAGCACCTATCTACCCTGAATC TAAGTGCTAACAGGAAAGGATGCCAGATTGCATGCCTGCTGATAAAGCCA CAGTTTGGACTGTCACTCAATCACCATCGTTCCTCCTGTGACTCAGTATA ACAAGATTGGGAGAATACTCTACAGTTCCTGATTCCCCCACAGAAGTGAA AGAGAATACTGCAACACACATTCAGTGTTCAGACTTCAGGGGAGTTGCCA AGTGATTGTTTTCTGTCTTGCCTGAATTTAAGCGTTAACAGGAAAGCTTT CCAGGTTGGGGATATTAAGAATAAATGAGTTGAGGAAGTTTGGGTTAGCA TACATTCACTTATCATATCATCCTTCCCTGGATCAATATGCAATGAGTGG GACAAAACCCTCAACTCCTGGCTTCCCCTTGGAGAAGGAAAAAGCTGGAG TGTGCATCCAGAATTTCAACTTTTCCCAGTCAGCCTGATGGACTGTTTTC This sequence will be \(S\) with \(n=500\)./docs/reference/apis/Thu, 07 Sep 2023 16:12:37 +0200/docs/reference/apis/Rust Rustdoc autodocumentation is generated with cargo doc --no-deps. main branch/docs/reference/matrices/Thu, 07 Sep 2023 16:12:37 +0200/docs/reference/matrices/The default matrices SymCurve uses for roll (\(\rho\)), twist (\(\Omega\)), and tilt (\(\tau\)) are listed on this page. The matrix sizes are all 4x4x4, where the values are indexed by nucleotide 3-mers as in the matrix \(M\) below: \[ M = \begin{bmatrix} \begin{bmatrix} M_{AAA} & M_{AAT} & M_{AAG} & M_{AAC} \\ M_{ATA} & M_{ATT} & M_{ATG} & M_{ATC} \\ M_{AGA} & M_{AGT} & M_{AGG} & M_{AGC} \\ M_{ACA} & M_{ACT} & M_{ACG} & M_{ACC} \end{bmatrix}, \\ \begin{bmatrix} M_{TAA} & M_{TAT} & M_{TAG} & M_{TAC} \\ M_{TTA} & M_{TTT} & M_{TTG} & M_{TTC} \\ M_{TGA} & M_{TGT} & M_{TGG} & M_{TGC} \\ M_{TCA} & M_{TCT} & M_{TCG} & M_{TCC} \end{bmatrix}, \\ \begin{bmatrix} M_{GAA} & M_{GAT} & M_{GAG} & M_{GAC} \\ M_{GTA} & M_{GTT} & M_{GTG} & M_{GTC} \\ M_{GGA} & M_{GGT} & M_{GGG} & M_{GGC} \\ M_{GCA} & M_{GCT} & M_{GCG} & M_{GCC} \end{bmatrix}, \\ \begin{bmatrix} M_{CAA} & M_{CAT} & M_{CAG} & M_{CAC} \\ M_{CTA} & M_{CTT} & M_{CTG} & M_{CTC} \\ M_{CGA} & M_{CGT} & M_{CGG} & M_{CGC} \\ M_{CCA} & M_{CCT} & M_{CCG} & M_{CCC} \end{bmatrix} \end{bmatrix} \] Roll \[ \rho^\psi = \begin{bmatrix} \begin{bmatrix} 0./privacy/Thu, 07 Sep 2023 17:19:07 +0200/privacy/