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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Related Experiment Video

Updated: Jun 3, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads.

Xiaofei Carl Zang1, Xiang Li2, Kyle Metcalfe3

  • 1Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.

Algorithms in Bioinformatics : ... International Workshop, WABI ..., Proceedings. WABI (Workshop)
|January 7, 2025
PubMed
Summary

Anchorage is a new tool for assembling DNA sequences using anchor-guided methods. It improves full-length sequence reconstruction from ultra-high depth sequencing data, especially with sequencing artifacts.

Keywords:
Applied computing → Molecular sequence analysisGenome assemblyLoopSeqanchor-guided assemblyde Bruijn graphsynthetic long reads

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Modern sequencing technologies incorporate sequence tags (anchors) to aid in full-length molecule reconstruction.
  • Synthetic long read (SLR) sequencing protocols like LoopSeq Solo generate ultra-high depth data, posing assembly challenges.
  • Existing assembly algorithms struggle with the complexity of anchor-enabled, high-coverage sequencing data.

Purpose of the Study:

  • To develop a novel assembler, Anchorage, specifically designed for anchor-guided assembly of ultra-high depth sequencing data.
  • To address the limitations of current methods in reconstructing full-length sequences from anchor-enabled data.

Main Methods:

  • Anchorage utilizes a kmer-based approach for accurate molecule length estimation.
  • The assembly problem is framed as finding an optimal path in a de Bruijn graph, guided by anchors.
  • A modified dynamic programming algorithm efficiently identifies the optimal path for sequence reconstruction.

Main Results:

  • Anchorage demonstrates superior performance compared to existing assembly methods in simulations and real-world data.
  • The assembler is particularly effective in handling sequencing artifacts, improving sequence reconstruction accuracy.
  • Anchorage successfully bridges the gap in assembling anchor-enabled sequencing data.

Conclusions:

  • Anchorage provides an effective solution for assembling anchor-enabled, ultra-high depth sequencing data.
  • The tool is expected to see widespread adoption as anchor-enabled sequencing technologies become more common.
  • Anchorage is publicly available, promoting further research and application in genomics.