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Bioinformatics

Bioinformatics. Bioinformatics. Bioinformatics is an applied science that uses computer programs to access molecular biology databanks to make inferences about the information contained within the data archives.

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Bioinformatics

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  1. Bioinformatics

  2. Bioinformatics • Bioinformatics is an applied science thatuses computer programs to access molecularbiology databanks to make inferences about theinformation contained within the data archives. • This lab introduces you to some of the maindatabanks, their applications, and programs. • You will learn how to retrieve information fromthe databases, and analyze the information toobtain useful knowledge about a DNA sequenceand its protein product.

  3. Why it’s useful • All of the information needed to build an organism is contained in its DNA. If we could understand it, we would know how life works. • Preventing and curing diseases like cancer (which is caused by mutations in DNA) and inherited diseases. • Curing infectious diseases (everything from AIDS and malaria to the common cold). If we understand how a microorganism works, we can figure out how to block it. • Understanding genetic and evolutionary relationships between species • Understanding genetic relationships between humans.

  4. Bioinformatics • PART I • You will search some of the most established public biological databanks using a query DNA sequence. • You will examine the predicted amino acid sequence from the nucleotide base sequence provided. • You will use this amino acid sequence to conduct a search for similar amino acid sequences in the database.

  5. Bioinformatics • PART II • You will utilize sequence data from your bacterial DNA PCR products to identify the bacteria from which you obtained this DNA. • To carry out this activity you will conduct a BLAST search on the Internet and identify the sequence that most closely matches your sequence. • We will do Part I using computers together in class. For Part II, you will work independently.

  6. The URL of ENTREZ, the NCBI databases, is: http://www.ncbi.nlm.nih.gov/sites/gquery

  7. I. Using an Example Sequence (Full Gene) to Do BLAST Searches • BLASTn is a search in which a nucleotide query sequence is compared with the contents of a nucleotide sequence database to find regions of sequences similar to regions of the original (query) sequence. • Matching sequences are called BLAST hits. • Database query: “given this DNA sequence, what sequences in the database are similar?”

  8. ORF Finder: Open Reading Frame Search • Regions of DNA that encode proteins are first transcribed into mRNA and then translated into protein. • In translation of mRNA into protein, codons of three nucleotides translate into an amino acid sequentially from the start until a stop signal is reached. • Start sequence ATG which codes for methionine (Met) • End sequence with a stop codon (TAA, TAG, or TGA).

  9. ORF Finder: Open Reading Frame Search • To determine the amino acid sequence of the protein directly from the DNA sequence the nucleotide that starts the translation and the stop signal must be determined. This sequence is the open reading frame (ORF). • There are six possible reading frames for each gene: three reading frames in the forward direction (5’ – 3’) and three reading frames in the reverse direction (3’ – 5’). The reading frame that results in the longest protein is usually the ORF that encodes the expressed protein.

  10. BLASTp • Blastp results are a one pair-wise alignment between the query sequence and sequences in the database. • The results are presented in a manner similar to a BLASTn query. The gi number, accession number, name of protein, score and E-value for the alignment is given. • Some of the hit sequences may have the letter “S” in the right hand column indicating that a structure associated with the sequence is on file in the Protein Data Bank (pdb).

  11. II. BLAST Search of Your PCR DNA Product. • For this activity you will work on your own to identify the organism in the database that is most similar to the bacteria from which you extracted your DNA. • To do this, you will be presented with the sequence data for your PCR product. • Remember the primers used targeted a 500 bp region of the gene that codes for the 16S ribosomal subunit.

  12. Laboratory Summary • Submit your Bioinfo_AssignmentWord document divided appropriately into its two parts (include headings to identify these): • • Include each of the requirements, with a brief title for each these. • • Answered questions, with headings.

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