<div dir="ltr">A different take from another AI (GPT-4o):<br><div class="gmail-w-full gmail-text-token-text-primary" dir="auto" style="border:0px solid rgb(227,227,227);box-sizing:border-box;width:1780px;font-family:ui-sans-serif,-apple-system,system-ui,"Segoe UI",Roboto,Ubuntu,Cantarell,"Noto Sans",sans-serif,Helvetica,"Apple Color Emoji",Arial,"Segoe UI Emoji","Segoe UI Symbol";font-size:14px"><div class="gmail-py-2 gmail-juice:py-[18px] gmail-px-3 gmail-text-base gmail-md:px-4 gmail-m-auto gmail-md:px-5 gmail-lg:px-1 gmail-xl:px-5" style="border:0px solid rgb(227,227,227);box-sizing:border-box;padding:18px 1.25rem;margin:auto;font-size:1rem;line-height:1.5rem"><div class="gmail-mx-auto gmail-flex gmail-flex-1 gmail-gap-3 gmail-text-base gmail-juice:gap-4 gmail-juice:md:gap-6 gmail-md:max-w-3xl gmail-lg:max-w-[40rem] gmail-xl:max-w-[48rem]" style="border:0px solid rgb(227,227,227);box-sizing:border-box;max-width:48rem;margin-left:auto;margin-right:auto;display:flex;font-size:1rem;line-height:1.5rem"><div class="gmail-group/conversation-turn gmail-relative gmail-flex gmail-w-full gmail-min-w-0 gmail-flex-col" style="border:0px solid rgb(227,227,227);box-sizing:border-box;display:flex;width:768px;min-width:0px"><div class="gmail-flex-col gmail-gap-1 gmail-md:gap-3" style="border:0px solid rgb(227,227,227);box-sizing:border-box"><div class="gmail-flex gmail-flex-grow gmail-flex-col gmail-max-w-full" style="border:0px solid rgb(227,227,227);box-sizing:border-box;display:flex;max-width:100%"><div dir="auto" class="gmail-min-h-[20px] gmail-text-message gmail-flex gmail-flex-col gmail-items-start gmail-whitespace-pre-wrap gmail-break-words gmail-[.text-message+&]:mt-5 gmail-juice:w-full gmail-juice:items-end gmail-overflow-x-auto gmail-gap-2" style="border:0px solid rgb(227,227,227);box-sizing:border-box;display:flex;min-height:20px;overflow-x:auto;width:768px"><div class="gmail-flex gmail-w-full gmail-flex-col gmail-gap-1 gmail-juice:empty:hidden gmail-items-end gmail-rtl:items-start" style="border:0px solid rgb(227,227,227);box-sizing:border-box;display:flex;width:768px"><div class="gmail-relative gmail-max-w-[70%] gmail-rounded-3xl gmail-bg-[#f4f4f4] gmail-px-5 gmail-py-2.5 gmail-dark:bg-token-main-surface-secondary" style="border:0px solid rgb(227,227,227);box-sizing:border-box;max-width:70%;border-radius:1.5rem;padding:0.625rem 1.25rem">is the human genome inherently compressed data</div></div></div></div></div></div></div></div></div><div class="gmail-w-full gmail-text-token-text-primary" dir="auto" style="border:0px solid rgb(227,227,227);box-sizing:border-box;width:1780px;font-family:ui-sans-serif,-apple-system,system-ui,"Segoe UI",Roboto,Ubuntu,Cantarell,"Noto Sans",sans-serif,Helvetica,"Apple Color Emoji",Arial,"Segoe UI Emoji","Segoe UI Symbol";font-size:14px"><div class="gmail-py-2 gmail-juice:py-[18px] gmail-px-3 gmail-text-base gmail-md:px-4 gmail-m-auto gmail-md:px-5 gmail-lg:px-1 gmail-xl:px-5" style="border:0px solid rgb(227,227,227);box-sizing:border-box;padding:18px 1.25rem;margin:auto;font-size:1rem;line-height:1.5rem"><div class="gmail-mx-auto gmail-flex gmail-flex-1 gmail-gap-3 gmail-text-base gmail-juice:gap-4 gmail-juice:md:gap-6 gmail-md:max-w-3xl gmail-lg:max-w-[40rem] gmail-xl:max-w-[48rem]" style="border:0px solid rgb(227,227,227);box-sizing:border-box;max-width:48rem;margin-left:auto;margin-right:auto;display:flex;font-size:1rem;line-height:1.5rem"><div class="gmail-flex-shrink-0 gmail-flex gmail-flex-col gmail-relative gmail-items-end" style="border:0px solid rgb(227,227,227);box-sizing:border-box;display:flex"><div style="border:0px solid rgb(227,227,227);box-sizing:border-box"><div class="gmail-pt-0.5 gmail-juice:pt-0" style="border:0px solid rgb(227,227,227);box-sizing:border-box;padding-top:0px"><div class="gmail-gizmo-bot-avatar gmail-flex gmail-h-6 gmail-w-6 gmail-items-center gmail-justify-center gmail-overflow-hidden gmail-rounded-full gmail-juice:h-8 gmail-juice:w-8" style="border:0px solid rgb(227,227,227);box-sizing:border-box;display:flex;height:2rem;width:2rem;overflow:hidden;border-radius:9999px"><div class="gmail-relative gmail-p-1 gmail-rounded-sm gmail-flex gmail-items-center gmail-justify-center gmail-bg-token-main-surface-primary gmail-text-token-text-primary gmail-h-8 gmail-w-8" style="border:0px solid rgb(227,227,227);box-sizing:border-box;display:flex;height:2rem;width:2rem;border-radius:0.125rem;padding:0.25rem"></div></div></div></div></div><div class="gmail-group/conversation-turn gmail-relative gmail-flex gmail-w-full gmail-min-w-0 gmail-flex-col gmail-agent-turn" style="border:0px solid rgb(227,227,227);box-sizing:border-box;display:flex;width:712px;min-width:0px"><div class="gmail-flex-col gmail-gap-1 gmail-md:gap-3" style="border:0px solid rgb(227,227,227);box-sizing:border-box"><div class="gmail-flex gmail-flex-grow gmail-flex-col gmail-max-w-full" style="border:0px solid rgb(227,227,227);box-sizing:border-box;display:flex;max-width:100%"><div dir="auto" class="gmail-min-h-[20px] gmail-text-message gmail-flex gmail-flex-col gmail-items-start gmail-whitespace-pre-wrap gmail-break-words gmail-[.text-message+&]:mt-5 gmail-juice:w-full gmail-juice:items-end gmail-overflow-x-auto gmail-gap-2" style="border:0px solid rgb(227,227,227);box-sizing:border-box;display:flex;min-height:20px;overflow-x:auto;width:712px"><div class="gmail-flex gmail-w-full gmail-flex-col gmail-gap-1 gmail-juice:empty:hidden gmail-juice:first:pt-[3px]" style="border:0px solid rgb(227,227,227);box-sizing:border-box;display:flex;width:712px;padding-top:3px"><div class="gmail-markdown gmail-prose gmail-w-full gmail-break-words gmail-dark:prose-invert gmail-light" style="border:0px solid rgb(227,227,227);box-sizing:border-box;max-width:none;font-size:1rem;line-height:1.75;width:712px"><p style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin:0px 0px 1.25em">The human genome can be thought of as inherently compressed in a biological sense because it uses a highly efficient system to store genetic information. Here are a few key points to understand this concept:</p><ol style="border:0px solid rgb(227,227,227);box-sizing:border-box;list-style-position:initial;margin:1.25em 0px;padding:0px 0px 0px 1.625em"><li style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin-bottom:0.5em;margin-top:0.5em;padding-left:0.375em"><p style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin:1.25em 0px"><span style="border:0px solid rgb(227,227,227);box-sizing:border-box;font-weight:600">DNA Structure</span>: The human genome consists of DNA, which is composed of four nucleotides (adenine, thymine, cytosine, and guanine). The sequence of these nucleotides encodes the genetic information.</p></li><li style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin-bottom:0.5em;margin-top:0.5em;padding-left:0.375em"><p style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin:1.25em 0px"><span style="border:0px solid rgb(227,227,227);box-sizing:border-box;font-weight:600">Coding vs. Non-coding Regions</span>: Only a small portion of the genome (about 1-2%) actually codes for proteins. The rest consists of non-coding regions, some of which have regulatory functions, while others are less understood or considered "junk" DNA. This means that a large portion of the genome does not directly contribute to the coding of proteins, suggesting an efficient way to store information where not all sequences are equally critical.</p></li><li style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin-bottom:0.5em;margin-top:0.5em;padding-left:0.375em"><p style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin:1.25em 0px"><span style="border:0px solid rgb(227,227,227);box-sizing:border-box;font-weight:600">Genetic Redundancy and Repetitive Elements</span>: The human genome contains many repetitive elements and sequences. Some sequences are repeated multiple times throughout the genome, and there are mechanisms to use these repetitions efficiently, akin to data compression in computational terms.</p></li><li style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin-bottom:0.5em;margin-top:0.5em;padding-left:0.375em"><p style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin:1.25em 0px"><span style="border:0px solid rgb(227,227,227);box-sizing:border-box;font-weight:600">Chromatin Structure</span>: DNA is wrapped around histone proteins to form nucleosomes, which further coil and fold into higher-order structures. This packaging not only helps to fit the large amount of DNA into the nucleus but also regulates gene expression and access to genetic information.</p></li><li style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin-bottom:0.5em;margin-top:0.5em;padding-left:0.375em"><p style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin:1.25em 0px"><span style="border:0px solid rgb(227,227,227);box-sizing:border-box;font-weight:600">Epigenetic Regulation</span>: Beyond the nucleotide sequence, epigenetic modifications (such as DNA methylation and histone modification) provide additional layers of information and regulation without altering the underlying DNA sequence. This can be viewed as another form of data compression, where additional information is overlaid on the genetic code.</p></li></ol><p style="border:0px solid rgb(227,227,227);box-sizing:border-box;margin:1.25em 0px 0px">While these biological mechanisms are not compression in the digital sense, they represent ways the genome efficiently stores and regulates vast amounts of information.</p></div></div></div></div></div></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, May 20, 2024 at 12:20 PM BillK via extropy-chat <<a href="mailto:extropy-chat@lists.extropy.org">extropy-chat@lists.extropy.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">On Mon, 20 May 2024 at 15:26, Will Steinberg via extropy-chat <<a href="mailto:extropy-chat@lists.extropy.org" target="_blank">extropy-chat@lists.extropy.org</a>> wrote:<br>><br>> @john: the human genome IS compressed data.<br>> _______________________________________________<br><br><br>Hi Will<br><br>Genetic researchers can compress the human genome.<br>BillK<br><br>I asked -<br>Is the human genome already compressed data, or can it be stored in a compressed format?<br><div><br></div><div>Perplexity Pro AI -</div><div><br></div><div>The human genome is not inherently compressed data, but it can be stored in a compressed format. The vast amount of genomic data generated by modern sequencing technologies necessitates efficient storage solutions, and various specialized compression algorithms have been developed to address this need.<br><br>### Compression Methods for Genomic Data<br><br>1. **SparkGC**:<br>   - SparkGC is an Apache Spark-based genome compression method designed to handle large collections of genomes efficiently. It uses Resilient Distributed Datasets (RDD) transformations to keep data active in memory throughout the compression process, significantly improving compression speed and scalability. SparkGC can compress 1100 human genomes on a common computer with just 24 GB of RAM, achieving the best compression ratio among state-of-the-art methods[1].<br><br>2. **Lossless DNA Compression Algorithm**:<br>   - This method specializes in compressing nucleotide sequence data in FASTA/multi-FASTA formats. It separates the headers and uses 7-Zip for compression, achieving a high compression ratio by leveraging the specific characteristics of DNA sequences[2].<br><br>3. **LZ77 and CTW Algorithms**:<br>   - A method combining the LZ77 algorithm with the context tree weighting (CTW) algorithm has been proposed to compress DNA data. This approach first converts DNA sequences into intermediate files before applying LZ77, resulting in significant reductions in compression and decompression times while maintaining a high compression rate[3].<br><br>4. **Neural Network-Based Compression (GeCo3)**:<br>   - GeCo3 uses a neural network metamodel to improve the compression ratio of DNA sequences. It benchmarks both reference-free and referential compression, showing consistent improvements over other state-of-the-art DNA compressors. This method is particularly useful for long-term storage and sequence analysis[4].<br><br>5. **FQSqueezer**:<br>   - FQSqueezer is a novel algorithm for compressing sequencing data, particularly FASTQ files. It uses prediction by partial matching (PPM) and dynamic Markov coder (DMC) algorithms, achieving better compression ratios than existing tools. However, it requires significant memory and time resources[5].<br><br>### Conclusion<br><br>The human genome can indeed be stored in a compressed format using specialized algorithms designed to handle the unique characteristics of genomic data. These methods significantly reduce the storage requirements and improve the efficiency of data handling in genomic research and applications.<br><br>Citations:<br>[1] <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04825-5" target="_blank">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04825-5</a><br>[2] <a href="https://www.mdpi.com/1999-4893/13/4/99" target="_blank">https://www.mdpi.com/1999-4893/13/4/99</a><br>[3] <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7688149/" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7688149/</a><br>[4] <a href="https://academic.oup.com/gigascience/article/9/11/giaa119/5974977" target="_blank">https://academic.oup.com/gigascience/article/9/11/giaa119/5974977</a><br>[5] <a href="https://www.nature.com/articles/s41598-020-57452-6" target="_blank">https://www.nature.com/articles/s41598-020-57452-6</a><br>[6] <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05500-z" target="_blank">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05500-z</a><br>[7] <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9337911/" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9337911/</a><br>[8] <a href="https://www.reddit.com/r/askscience/comments/637gyu/is_dna_compressed/" target="_blank">https://www.reddit.com/r/askscience/comments/637gyu/is_dna_compressed/</a><br>[9] <a href="https://arxiv.org/abs/2006.02232" target="_blank">https://arxiv.org/abs/2006.02232</a><br>[10] <a href="https://www.sciencedirect.com/science/article/pii/S2666389922001738" target="_blank">https://www.sciencedirect.com/science/article/pii/S2666389922001738</a><br>[11] <a href="https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1260531/full" target="_blank">https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1260531/full</a><br>[12] <a href="https://en.wikipedia.org/wiki/Compression_of_genomic_sequencing_data" target="_blank">https://en.wikipedia.org/wiki/Compression_of_genomic_sequencing_data</a><br>[13] <a href="https://github.com/rajatdiptabiswas/dna-compression" target="_blank">https://github.com/rajatdiptabiswas/dna-compression</a><br>[14] <a href="https://arxiv.org/abs/2401.14025" target="_blank">https://arxiv.org/abs/2401.14025</a><br>[15] <a href="https://www.sciencedirect.com/science/article/pii/S1877050916318762" target="_blank">https://www.sciencedirect.com/science/article/pii/S1877050916318762</a><br>[16] <a href="https://www.illumina.com/documents/products/whitepapers/whitepaper_datacompression.pdf" target="_blank">https://www.illumina.com/documents/products/whitepapers/whitepaper_datacompression.pdf</a><br>[17] <a href="https://arxiv.org/abs/2311.01431" target="_blank">https://arxiv.org/abs/2311.01431</a><br>[18] <a href="https://blog.chiariglione.org/genome-is-digital-and-can-be-compressed/" target="_blank">https://blog.chiariglione.org/genome-is-digital-and-can-be-compressed/</a><br>[19] <a href="https://pubmed.ncbi.nlm.nih.gov/37018338/" target="_blank">https://pubmed.ncbi.nlm.nih.gov/37018338/</a><br>[20] <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02443-7" target="_blank">https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02443-7</a></div>------------------------------------<br></div>
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