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    Chair of Bioinformatics

    Molecular Biology

    We give here a quick and easy guide to do Molecular Biology by computer. There is also the real lecture ("Molecular Biology" for all Master students of any semester), Tue, Wed and Fri at 9:00 in A102.

    So using the computer you always need some data to do molecular biology. This is solved here by giving you sample sequences. For each step of analysis (each lecture in real life) you get some test data to process. Next you need the computer. However, we are in the age of the internet. So a link to a program doing the calculation will be fine and these are also given for each lecture. Now bring both together and get your own result!

     

     

    Lecture 1

    Tutorial 1: BLAST

    Take the DNA sequences from the word files and run a Nucleotide BLAST search (for the first sequence select the Human genomic + transcript database): https://blast.ncbi.nlm.nih.gov/Blast.cgi
    Which genes are searched?

    Click here to download the sequences:

    - exercise1Seq1

    - exercise1Seq2

    - exercise1Seq3

     

    To learn more about BLAST and how to use it quiet well have a look on the NCBI tutorials on youtube:

    Focus especially on the output parameters. What is the difference between the E- and p-Value? How do you interprete a high E-value?

    https://www.youtube.com/watch?v=2FW1dk5YQ3I&list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq&index=3

    https://www.youtube.com/watch?v=JKD5laNtwSc&list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq&index=5&t=0s

     

    Sequence 1

    - a gene related to cancer

    Sequence 2

    - a gene coding for a hypothetical protein

    Sequence 3

    - a viral nucleotide sequence

    For more detailed information open the Results file and follow the included links.

     

    Also make familiar with the new results format:

    https://www.youtube.com/watch?v=mKC0xptQ_AY&list=PLH-TjWpFfWrtjzMCIvUe-YbrlIeFQlKMq

     

    For further genomic online tools have a look at the UCSC Genome Browser https://genome.ucsc.edu/

    Lecture 2

    Tutorial 2: RNA

    1. lin-4 miRNA

    The first discoverd microRNA is the lin-4 miRNA. Search this miRNA in the Rfam database. Does the lin-4 miRNA occur in humans or mice?

    Take the RNA sequence from the human lin-4 miRNA and perform an analysis with the RNA Analyzer.  Which structure does the miRNA show? What does a negative energy mean?

     

    2. Hammerhead_1

    Take the sequence of the  Hammerhead_1 from Clonochis sinensis and execute an analysis with RNAfold. Have a look at the dot plot containing the base pair probabilities and interprete it. What is a dot plot at all?

     

    Results

     

    Links:

    - RFAM
    - Riboswitch Finder
    - mfold
    - RNAfold
    - RNA Analyzer

    Lecture 3

    Tutorial 3: Proteins

    1. Take the unknown  amino acid sequenceand run a Protein BLAST  search (Algorithm: Quick BLASTP) to identify the organism the protein sequence is originated from.

    Secondly, run a PSI-BLAST with 3 iterations to identify the supposed protein function. Only select the top 100 sequences. (Hint: the "Run PSI-Blast iteration X" is placed under descriptions). What does the yellow highlighting mean?

     

    2. Search for the proteins BRCA1_Human, BRCA2_Human and BRCA2_Mouse in the UniProt  database. Use the Align tool and align BRCA2_Human with BRCA1_Human and BRCA2_Mouse, respectively. Is BRCA2 more related to BRCA1 from human or BRCA2 from mice? Which information about the protein sequences do you also get?

     

    For this protein alignment have a look on the really short video tutorials!

    https://www.youtube.com/channel/UCkCR5RJZCZZoVTQzTYY92aw

    https://www.youtube.com/watch?v=IAYFLfPQ0Gs

     

    3. Take the protein sequence from BRCA1_Human and run a sequence analysis with SMART.Which domains do you get for BRCA1 from human? How many phosphorylations does the protein show?

     

    4. Take this amino acid sequencefrom the lecture and run a BLASTsearch. You will get the histone acetyltransferase KAT2A from homo sapiens as result.

    Verify your result by scanning the sequence using Prosite. Which motifs are uncovered and which functions do they have? Verify it a second time using AnDom. Note, that you need the Protein-Identifier for human KAT2A (Q92830 from UniProt).

    Go to theProtein Data Bankand search for KAT2A. You will find 6 structures. Download the structure file of the 5TRL crystal structure as PDB Format or click here and visualize the 3D structure using the RasMolsoftware. Generate a Ramachandran plot for 5tlr using the Uppsala Ramachandran Server.

    To interpret the Ramachandran plot have a look at this video.

     

    Results

     

    Links:

    - PDB
    - UniProt
    - SMART
    - SCOP
    - CATH
    - AnDOM
    - SwissModel
    - Prosite
    - Rasmol
    - Ramachandran-Plot