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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
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Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Blast Quantification Using Hopkinson Pressure Bars
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Blast Quantification Using Hopkinson Pressure Bars

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Curated BLAST for Genomes.

Morgan N Price1, Adam P Arkin1

  • 1Lawrence Berkeley National Laboratory, Berkeley, California, USA.

Msystems
|April 5, 2019
PubMed
Summary
This summary is machine-generated.

Curated BLAST for Genomes identifies candidate genes for specific biological processes or enzymatic activities. This tool overcomes limitations of automated annotations by comparing genome proteins to experimentally characterized ones, improving gene discovery.

Keywords:
annotation

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Predicting microbial capabilities from genome sequences is crucial for understanding organismal functions.
  • Automated gene annotations often provide vague or inaccurate functional predictions.
  • Identifying specific genes responsible for known capabilities is a common challenge in genomics.

Purpose of the Study:

  • To develop a tool that accurately identifies candidate genes for specific biological processes or enzymatic activities within a genome.
  • To provide an alternative to potentially unreliable automated gene annotations.
  • To facilitate the discovery of genes involved in known organismal capabilities.

Main Methods:

  • Curated BLAST searches a database of over 100,000 characterized proteins based on user queries (e.g., enzyme name, EC number).
  • It compares query-matched characterized proteins against predicted proteins in the target genome.
  • The tool also analyzes the six-frame translation of the genome to account for potential gene model errors.

Main Results:

  • Curated BLAST successfully identifies candidate genes for specific functions, even when automated annotations fail.
  • The method is efficient and highlights relevant genes missed by standard annotation pipelines.
  • It provides a list of candidate genes based on similarity to experimentally validated proteins.

Conclusions:

  • Curated BLAST is a valuable tool for functional gene discovery in genomics.
  • It offers a reliable method for predicting organismal capabilities and identifying involved genes.
  • The tool enhances the accuracy and completeness of genomic functional analysis.