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Related Concept Videos

Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
Gene Conversion02:08

Gene Conversion

Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
From DNA to Protein03:06

From DNA to Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

ALTER: program-oriented conversion of DNA and protein alignments.

Daniel Glez-Peña1, Daniel Gómez-Blanco, Miguel Reboiro-Jato

  • 1Departamento de Informática, Universidad de Vigo, 32004 Ourense, Spain.

Nucleic Acids Research
|May 5, 2010
PubMed
Summary
This summary is machine-generated.

ALTER is a new web tool for converting multiple sequence alignment formats, focusing on mainstream programs. It also removes identical sequences and offers programmatic access via a web service.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Multiple sequence alignment (MSA) is crucial for analyzing biological sequences.
  • Existing tools often focus on specific formats, limiting interoperability.
  • Standardizing MSA formats is essential for integrating diverse analysis pipelines.

Purpose of the Study:

  • To develop a versatile web-based tool for seamless conversion between various multiple sequence alignment formats.
  • To enhance data processing by enabling the identification and removal of redundant sequences during format transformation.
  • To provide both a user-friendly interface and a programmatic API for broad accessibility.

Main Methods:

  • Development of a web application (ALTER) accessible via a graphical user interface.
  • Implementation of a Representational State Transfer (REST) web service for programmatic access.
  • Focus on supporting mainstream alignment and analysis program specifications for broad compatibility.

Main Results:

  • ALTER successfully transforms sequences between multiple alignment formats.
  • The tool effectively identifies and removes identical sequences, streamlining datasets.
  • Both the web interface and API are publicly available, facilitating widespread adoption.

Conclusions:

  • ALTER offers a flexible and user-friendly solution for multiple sequence alignment format conversion.
  • Its focus on mainstream programs and deduplication capabilities addresses key challenges in bioinformatics workflows.
  • The availability of both a front-end and an API promotes integration and usability in diverse research settings.