Bioinformatics

• what is bioinformatics?

  using computer technology to collect, store, analyse and disseminate biological data and information
• why do we need bioinformatics?

  growth of databases of genetic information

  sequencing cost per human genome
• what can bioinformatic be used for?

  genome sequence and annotation

  protein structure and molecular binding

  DNA identification

  Omics studies
• what is an omics?

  large scale study of various biomoles
• what is genomics?

  DNA

  whole genome sequencing, microarray
• what is epigenomics?

  DNA modification

  Whole genome bisulfite sequencing
• what is transcriptomics?

  RNA

  RNA-sequencing
• What is proteomics?

  protein

  mass spectrometry
• what is metabolomics?

  metabolite

  mass spectrometry
• what is a metabolite: compounds involved in metabolism sustaining chemical reactions in organisms
• what bioinformatics techniques range from website to programming?

  Finding/analysing data using website

  data analysis through software

  developing tools and resources
• what are common problems for bioninformatics beginners?

  larger number of tool available

  Most tools and databases are not very user-friendly

  The outputs can look intimidating

  many different file formats
• what does DNA barcoding allow?

  species identification
• How to carry out DNA barcoding?

  PCR
• describe DNA barcoding

  Cost effective

  genes regions that are similar within the same species and distinct across different species
• What are commonly used genes in DNA barcoding?

  Animals: MT-CO1, 16s rRNA

  Fungi: ITS (internal transcribed spacer)

  Bacteria: 16S rRNA or 18S rRNA
• when would use DNA barcodes?

  food fraud detection

  identifying pollen

  pathogen surveillance
• what file formate is given to a DNA barcode?

  FASTA formate
• where is the sequence ID in FASTA format?

  first part until first space
• what is a GenBank file format?

  stores more information than a FASTA file
• What is BLAST?

  Bioinformatics software.
• what is a search?

  a database or perform a search to describe the process of looking for specific information in a database
• what is a query?

  The formal and structured request for data in database. Often used interchangeably with search. IN BLAST, it refers to your input sequence
• What is your subject (BLAST database)?

  The sequences that your query sequence is compared to
• what is the format for phylogenetic trees in DNA barcoding?

  Newick format
• what is a clade?

  a group of organisms that includes a single ancestor and all of its descendent
• What is a branch?

  Shows the path of transmission of genetic information from one generation to the next; the longer the lines, the more genetic change (or divergence) has occurred. The branch length are usually the number of genetic changes per site (i.e. if 1 base difference for a 100-base sequence, the length will be 0.01) .
• what is a sequence alignment?

  needed to make phylogenetic tree, uses a CLUSTAL file format
• what does a sequence aligment mean?

  A way of arrange amino acids or nucleotides sequences to identify regions of similarity
• what is a primary key (database)?

  A unique ID for identifying an entry in a table in a database. Minor technical difference to Accession number
• what are the fields?

  A set of attributes
• what us a retrieve (database)?

  identifying and extracting data from a database
• what is accession number (database):

  unique IDs used in database
• what is a genecard?

  a human gene database with extensive information on each gene
• What is a protein data bank (PDB) format used for?

  Store infomation on protein structure