Osnova sekce

  • Sequence comparison and translation

    • Comparisons of nucleotide sequences - (multiple)alignment

      Comparison is analogous to proteins. It is recommended to change substitution matrix.

      Multiple (or pairwise) alignments: Multalin

    • EX_0 Stránka

    • TranslationObr%C3%A1zek1.jpg

      =translation of nucleotide sequence into amino acids (protein)based on the genetic code

      SMS suite/ Translate → suitable only for full CDS (or when know ORF)

      NCBI/ORFfinder → suitable for translation of any nucleotide sequence, looking for ORFs

    • ex1: unknown sequnece (ORF) Stránka
    • Ex1-solution Stránka
    • ex2: unknown sequnece (ORF) Stránka
    • Ex2-solution Stránka

    • Unknown sequence identification

      BLASTn (searching nucleotide databases for similar nucleotide sequences)

    • DNA sequencing

      "Classic" Sanger´s sequencing (.scf, .abi, .ab1)

    • chromas Soubor
    • Ex3: unknown sequence.ab1 Soubor

      This (.ab1) is "unsupported" format, needs to be saved and then opened in chromas.

    • Detection of "vector contamination" in unknown sequence

      VecScreen

      Removing of "vector contamination" in unknown sequence

      SMS/Range Extractor

    • HW6 Úkol
    • HW6-unknown sequence.ab1 Soubor
    • Lesson 6 -pdf Soubor