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MyCLADE: a multi-source domain annotation server for sequence functional exploration.

Riccardo Vicedomini1,2, Clémence Blachon1, Francesco Oteri1

  • 1Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris 75005, France.

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Summary
This summary is machine-generated.

MyCLADE is a webserver for functional profiling of genomic and metagenomic sequences. It aids in understanding protein domain architectures using Pfam domain models.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genomic and metagenomic databases are rapidly expanding, necessitating efficient tools for sequence analysis.
  • Accurate functional profiling of these sequences against specific targets is crucial for biological discovery.

Purpose of the Study:

  • To introduce MyCLADE, a user-friendly webserver for targeted functional profiling of genomic and metagenomic sequences.
  • To provide a tool that utilizes a database of probabilistic models of Pfam domains for domain annotation.

Main Methods:

  • MyCLADE employs the MetaCLADE multi-source domain annotation strategy, modeling domains using multiple probabilistic profiles.
  • The webserver accepts protein sequences and optional target domains/clans, generating domain architectures.
  • It integrates with Pfam and QuickGO databases for comprehensive information retrieval.

Main Results:

  • MyCLADE provides detailed domain architectures for input protein sequences.
  • Annotation quality is supported by E-value, bit-score, probability scores, and sequence logos.
  • The tool facilitates targeted functional profiling against user-defined or all Pfam domains.

Conclusions:

  • MyCLADE offers an accessible and effective solution for the functional exploration of large-scale genomic and metagenomic data.
  • The webserver aids researchers in understanding protein domain composition and function.
  • Its integration with established databases enhances its utility for biological research.