Search this site
Embedded Files
Bioinformatics Final Project
  • Introduction
  • Materials & Methods
  • Results & Discussion
    • Adjusting for GC bias in the read-counts
    • Adjusting for origin of replication bias
    • HMM based CN prediction
  • References
Bioinformatics Final Project
  • Introduction
  • Materials & Methods
  • Results & Discussion
    • Adjusting for GC bias in the read-counts
    • Adjusting for origin of replication bias
    • HMM based CN prediction
  • References
  • More
    • Introduction
    • Materials & Methods
    • Results & Discussion
      • Adjusting for GC bias in the read-counts
      • Adjusting for origin of replication bias
      • HMM based CN prediction
    • References
      • Barrick, J. E., Colburn, G., Deatherage, D. E., Traverse, C. C., Strand, M. D., Borges, J. J., Knoester, D. B., Reba, A., & Meyer, A. G. (2014). Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics, 15(1), 1039. https://doi.org/10.1186/1471-2164-15-1039

      • Brynildsrud, O., Snipen, L.-G., & Bohlin, J. (2015, February 1). CNOGpro: Detection and quantification of cnvs in prokaryotic whole-genome sequencing data. OUP Academic. https://academic.oup.com/bioinformatics/article/31/11/1708/2365681%20

      • Chen, Y.-C., Liu, T., Yu, C.-H., Chiang, T.-Y., & Hwang, C.-C. (2013, April 29). Effects of GC bias in next-generation-sequencing data on de Novo Genome Assembly. PloS one. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3639258/

      • Copy number variation (CNV). Genome.gov. (n.d.). https://www.genome.gov/genetics-glossary/Copy-Number-Variation

      • Lai D, Ha G, Shah S (2023). HMMcopy: Copy number prediction with correction for GC and mappability bias for HTS data. doi:10.18129/B9.bioc.HMMcopy, R package version 1.44.0, https://bioconductor.org/packages/HMMcopy.

      • Pös, O., Radvanszky, J., Buglyó, G., Pös, Z., Rusnakova, D., Nagy, B., & Szemes, T. (2021, October). DNA copy number variation: Main characteristics, evolutionary significance, and pathological aspects. Biomedical journal. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8640565/

      • Tammi, Dr. M. T. (n.d.). CNOGpro. https://bioinformaticshome.com/tools/cnv/descriptions/CNOGpro.html#google_vignette

      • Zhang, H., Zeidler, A. F. B., Song, W., Puccia, C. M., Malc, E., Greenwell, P. W., Mieczkowski, P. A., Petes, T. D., & Argueso, J. L. (2013, March). Gene copy-number variation in haploid and diploid strains of the yeast saccharomyces cerevisiae. Genetics. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583998/

      • Syeda AH, Dimude JU, Skovgaard O and Rudolph CJ (2020) Too Much of a Good Thing: How Ectopic DNA Replication Affects Bacterial Replication Dynamics. Front. Microbiol. 11:534. doi: 10.3389/fmicb.2020.00534

Report abuse
Page details
Page updated
Report abuse