A degenerate symbol over an alphabet Σ is a non-empty subset of Σ, and a sequence of such symbols is a degenerate string. We investigate the exact computation of maximal degenerate palindromes with gaps and mismatches. We present an algorithm which, given a degenerate string of length n and natural number parameters g and m, efficiently detects exact maximal palindromes with a gap size ≤g, and ≤m permitted mismatches. We show that it can be done in O(k|Σ|(k+log⁡|Σ|)+(k+g+m)n) time and O((g+m)n) space, where k represents an upper bound on the number of degenerate symbols contained in the string. Furthermore, we also show that the problem of factorisation a string into maximal degenerate palindromes with gaps and mismatches can also be done in O(k|Σ|(k+log⁡|Σ|)+(k+g+m)n) time and O((g+m)n) space. An inverted repeat is a specific type of palindrome which refers to a nucleotide sequence followed by its reverse complement. Our results can also be used to find maximal inverted repeated sequences with gaps and mismatches, where changing the structure of palindromes to inverted repeats does not affect the overall running time. Finally we demonstrate our algorithm on several strains of SARS-CoV-2, and quantify the number of inverted repeats found with ≤0,1,2 mismatches and ≤0,10,100 gap size.

BACKGROUND: An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have been linked with countless possible functions. Many international consortia provide a comprehensive description of common genetic variation making alternative sequence representations, such as IUPAC encoding, necessary for leveraging the full potential of such broad variation datasets. RESULTS: We present IUPACPAL, an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences allowing also for potential mismatches and gaps in the inverted repeats. CONCLUSION: Within the parameters that were tested, our experimental results show that IUPACPAL compares favourably to a similar application packaged with EMBOSS. We show that IUPACPAL identifies many previously unidentified inverted repeats when compared with EMBOSS, and that this is also performed with orders of magnitude improved speed.

Spin-transfer torque magnetic random access memory (STT-MRAM) is a novel, magnetic memory technology that leverages the base platform established by an existing 100+nm node memory product called MRAM to enable a scalable nonvolatile memory solution for advanced process nodes. STT-MRAM features fast read and write times, small cell sizes of 6F 2 and potentially even smaller, and compatibility with existing DRAM and SRAM architecture with relatively small associated cost added. STT-MRAM is essentially a magnetic multilayer resistive element cell that is fabricated as an additional metal layer on top of conventional CMOS access transistors. In this review we give an overview of the existing STT-MRAM technologies currently in research and development across the world, as well as some specific discussion of results obtained at Grandis and with our foundry partners. We will show that in-plane STT-MRAM technology, particularly the DMTJ design, is a mature technology that meets all conventional requirements for an STT-MRAM cell to be a nonvolatile solution matching DRAM and/or SRAM drive circuitry. Exciting recent developments in perpendicular STT-MRAM also indicate that this type of STT-MRAM technology may reach maturity faster than expected, allowing even smaller cell size and product introduction at smaller nodes.