Osnova sekce


    • Searching for protein motives and domains

      Searching databases for typical protein motifs/conserved domains enables the annotation of functional units in proteins, providing insights into sequence/structure/function relationships.

      Conserved domain database: NCBI/CD

      Other databases for domain search: SMART, InterPro

    • Signal peptides

      The prediction of protein localization by recognizing signal peptide on the protein N-terminus. SignalP 

    • Prediction of transmembrane helices

      Prediction is based on amino acid hydrophobicity and probability.

      Hydrofobicity profile: Expasy/ProtScale

      Transmembrane helices prediction: TMHMM, Phobius, TopCons (multiple programs consensus), CCTOP

      Figures: PROTTER

    • BLAST- searching for similarity

      (Basic Local Alignment Search Tool)

      Based on short parts of the query sequence program searches for similar sequences using „substitution matrix“, which defines the score of potential alignments. 

      NCBI/BLAST  tutorial: 

      (UniProtKB/BLAST)

    • Example of substitution matrix Stránka
    • Lesson 3 -pdf Soubor
    • HW3 : Protein analyses, similarity Úkol