bioinforma2cs is done on Mac OS or Linux. – Linux and Mac OS are both based on Unix, so are much more similar to one another than either is with Windows. • Virtual Machines: Possible to run Linux on top of your Windows installa2on – the QIIME Virtual Box comes pre-‐installed with many of the tools we’ll use in this course. – h2p://qiime.org/install/virtual_box.html
binary numbers • In plain text files, the binary numbers encode for human readable text (ASCII encoding) • In contrast, a “binary” file is usually simply meant to encode a file that doesn’t represent human readable text.
• Easier to transfer between programs • Don’t need a special program to ‘decode’ the informa2on. • Examples: fasta, newick, PDB, json, biom, tab-‐ separated text
as tables (or spreadsheets) • Lines oXen represent records, and values are separated by delimiters: oXen tabs, spaces, or commas (I usually prefer tab-‐delimited text, and these are standard output formats from MS Excel and Google Docs). • These oXen contain headers lines, and some2mes contain comment lines. • Doesn’t work well for hierarchical data (e.g. trees), or when a certain field might contain different numbers of values.
to: • Show line numbers • Show invisibles (i.e., spaces): many programs treat space and tab characters differently, so it’s useful to see what a space character in a text file actually represents. • Define tab characters as some number of spaces • Choose line ending types • Use regular expressions for search/replace
Garland Science 2008) The Central Dogma of Molecular Biology DNA: an informa2on archive RNA: an informa2on carrier * these are func2onal molecules some2mes too protein: func2onal molecules
a large component of human skin • RuBisCO: a key enzyme in photosynthesis • Cholera toxin: a six-‐protein complex responsible for the disease state associated with cholera • Green fluorescent protein: jellyfish protein responsible for bioluminescence (and an extremely useful protein in biotechnology)
a binary digit • A byte is 8 bits (so what’s the largest number that can be represented in one byte?) • kilobyte (KB) is 1024 bytes, megabyte (MB) is 10242 bytes, gigabyte (GB) is 10243 bytes. • Why 1024? 210 = 1024, so approxima2on of the SI kilo prefix.
with C! RNA: A pairs with U; G pairs with C *A U in an RNA molecule will pair with an A in a DNA molecule; a T in a DNA molecule with pair with an A in an RNA molecule.
Garland Science 2008) The Central Dogma of Molecular Biology DNA: an informa2on archive RNA: an informa2on carrier * these are func2onal molecules and informa2on archive molecules in certain cases protein: func2onal molecules
Point muta2ons • synonymous – Results in the same amino acid sequence • non-‐synonymous – Results in different amino acid sequence • Inser2on/dele2ons (or indels) • Possible change of reading frame. Muta2ons rates (par2ally due to repair mechanisms) are low to ensure gene2c stability: in bacteria 1 nucleo2de change per 109 nucleo2des per cell genera2on. Muta%on
ACTAGCAT ACTAGTAT TCAATGTT TCCATGTT ACCAGGTT Time The random accumula2on of mutaFons (changes to gene sequences over evolu2onary 2me) gives us informa2on for iden2fying and comparing organisms.
mechanism: “survival of the fioest” or the “Preserva2on of Favoured Races in the Struggle for Life” muta2ons are always random, but they can some2mes result in an adap2ve change
fitness of the organism): rare, but likely to be propagated selec2vely neutral: may or may not be propagated deleterious (i.e., result in decreased fitness of the organism): unlikely to be propagated
Red blood cells assume an abnormal, rigid shape and exhibit reduced flexibility. These sickle-‐shaped cells build up in veins and capillaries, and obstruct blood flow causing pain and 2ssue damage. hop://www.nature.com/scitable/topicpage/sickle-‐cell-‐anemia-‐a-‐look-‐at-‐global-‐8756219
The sickle cell trait confers malaria resistance (although the mechanism isn’t fully understood), so more individuals with the trait will survive to reproduce and pass on the mutant gene.
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