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Saturday, January 29, 2022

BIOINFORMATICS TOOLS

Proteomics Tools

Protein Sequence Analysis and Function Prediction

  • ProtParam – Allows the computation of various physical and chemical parameters for a given protein sequence.
  • PEAKS CMD – It can perform de novo sequencing, protein identification, multi-engine protein identification,
    PTM search, sequence homology searching and quantification.
  • PEAKS Studio Xpro – A software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post-translational modifications (PTMs) and sequence variants (mutations), and peptide/protein de novo sequencing. (Commercial)

  • PANTHER-PSEP – Estimates the likelihood of a particular nonsynonymous (amino-acid changing) coding SNP to cause a functional impact on the protein.
  • ProtScale – It can compute and represent the profile produced by any amino acid scale on a selected protein.
  • PredictProtein – Service for protein structure prediction, protein sequence analysis, protein function prediction, protein sequence alignments, bioinformatics.
  • MutationTaster – Identifies disease-causing ability of sequence alterations.
  • MuPIT Interactive – Mapping variant positions to annotated, interactive 3D structures.

  • LS-SNP – An annotated database of SNPs. Currently only coding non-synonomous SNPs found in human genes are included. 

  • PeCop – Predicting Persistently Conserved Positions.

Protein Domain Prediction

  • SMART@EMBL – The web server is used for the identification and analysis of protein domains within protein sequences..
  • MEME – Motif-based sequence analysis tools.
  • InterPro@EBI – Protein domain and family classification database.
  • TMHMM 2.0 –  Web server for the prediction of transmembrane helices in proteins.

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