SARS-COV2 sequence generation by applying deep learning techniques on amino acid sequences (sequence to sequence encoder-decoder, GAN)

https://www.ncbi.nlm.nih.gov/protein/YP_009724390.1

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8056063/ https://www.mdpi.com/1420-3049/26/9/2622/pdf https://www.nature.com/articles/s42003-021-01754-6 https://www.nature.com/articles/s41401-020-0485-4 https://www.nature.com/articles/s41586-020-2895-3 https://www.sciencedirect.com/science/article/pii/S2405844021006757 https://www.tensorflow.org/addons/tutorials/networks_seq2seq_nmt https://arxiv.org/pdf/2008.11790.pdf https://www.nature.com/articles/s41579-021-00573-0#Sec3 https://pubmed.ncbi.nlm.nih.gov/33423311/

https://www.mdpi.com/2076-2607/9/5/1035/pdf https://virological.org/t/recent-evolution-and-international-transmission-of-sars-cov-2-clade-19b-pango-a-lineages/711 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709189/ https://www.ecdc.europa.eu/sites/default/files/documents/SARS-CoV-2-variant-multiple-spike-protein-mutations-United-Kingdom.pdf https://www.cell.com/cell/pdf/S0092-8674(20)30820-5.pdf https://covariants.org/variants https://www.nature.com/articles/s41598-021-96950-z https://www.nature.com/articles/s41467-020-19843-1 https://journals.asm.org/doi/10.1128/mBio.01188-21 http://www.cryst.bbk.ac.uk/education/AminoAcid/the_twenty.html

https://openaccess.thecvf.com/content_CVPR_2020/papers/Alharbi_Disentangled_Image_Generation_Through_Structured_Noise_Injection_CVPR_2020_paper.pdf

https://www.frontiersin.org/articles/10.3389/fimmu.2021.725240/full

https://github.com/MarisaKirisame/unroll_gan/blob/master/main.py https://github.com/andrewliao11/unrolled-gans/blob/master/unrolled_gan.ipynb

1. conda create --name clade_pred python=3.9
2. conda activate clade_pred
3. pip install tensorflow-gpu pandas matplotlib bio h5py scikit-learn nltk python-Levenshtein

https://www.tensorflow.org/guide/keras/rnn

https://aclanthology.org/2020.lrec-1.576.pdf https://dafx2020.mdw.ac.at/proceedings/papers/DAFx20in21_paper_12.pdf https://en.wikipedia.org/wiki/Gibbs_sampling http://people.csail.mit.edu/andyyuan/docs/interspeech-16.audio2vec.paper.pdf https://arxiv.org/pdf/2108.11992.pdf

https://github.com/nextstrain/ncov/blob/master/defaults/clade_emergence_dates.tsv

https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/index.html

Data from this analysis have been downloaded from GISAID (https://www.gisaid.org/help/publish-with-data-from-gisaid/)

• Khare, S., et al (2021) GISAID’s Role in Pandemic Response. China CDC Weekly, 3(49): 1049-1051. doi: 10.46234/ccdcw2021.255 PMCID: 8668406
• Elbe, S. and Buckland-Merrett, G. (2017) Data, disease and diplomacy: GISAID’s innovative contribution to global health. Global Challenges, 1:33-46. doi:10.1002/gch2.1018 PMCID: 31565258
• Shu, Y. and McCauley, J. (2017) GISAID: from vision to reality. EuroSurveillance, 22(13) doi:10.2807/1560-7917.ES.2017.22.13.30494 PMCID: PMC5388101