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Related Concept Videos

Elements and Compounds01:27

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Pure substances consist of only one type of matter. A pure substance can be an element or a compound. An element consists of only one type of atom, while a compound consists of two or more types of atoms held together by a chemical bond.
Elements
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Lesson: Translation
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The periodic table arranges atoms based on increasing atomic number so that elements with the same chemical properties recur periodically. When their electron configurations are added to the table, a periodic recurrence of similar electron configurations in the outer shells of these elements is observed. Because they are in the outer shells of an atom, valence electrons play the most important role in chemical reactions. The outer electrons have the highest energy of the electrons in an atom...
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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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Pure substances consist of only one type of matter. A pure substance can be an element or a compound. An element consists of only one type of atom, while a compound consists of two or more types of atoms held together by a chemical bond. Elements are classified as atomic or molecular based on the nature of their basic units.
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Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
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PITDB: a database of translated genomic elements.

Shyamasree Saha1, Eleni A Chatzimichali1, David A Matthews2

  • 1School of Biological and Chemical Sciences, Queen Mary University of London, Mile End, London E1 4NS, UK.

Nucleic Acids Research
|July 28, 2018
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Summary
This summary is machine-generated.

PITDB is a new database for translated genomic elements (TGEs) found using proteomics informed by transcriptomics (PIT). It aids researchers in identifying novel protein variants and constructing proteomes for diverse species.

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Proteomics informed by transcriptomics (PIT) integrates RNA-seq and mass spectrometry.
  • Canonical proteome databases may miss sample-specific or novel translated genomic elements (TGEs).

Purpose of the Study:

  • To introduce PITDB, a freely available database for TGEs identified through PIT experiments.
  • To provide a centralized resource for sharing and accessing PIT-derived data.

Main Methods:

  • Assembling transcripts from RNA-seq reads to build sample-specific amino acid sequence libraries.
  • Searching acquired mass spectra against these libraries to detect TGEs.
  • Curating and organizing TGE data with supporting evidence and confidence levels.

Main Results:

  • PITDB currently hosts over 74,000 distinct TGEs across four species.
  • The database is supported by over 600,000 peptide spectrum matches.
  • Includes TGEs ranging from known proteins to novel molecules and splice isoforms.

Conclusions:

  • PITDB offers a valuable resource for researchers utilizing PIT.
  • Facilitates the discovery and analysis of novel and variant translated genomic elements.
  • Supports proteome construction for both model and lesser-studied organisms.