Term
| What roles must Bioinformatics fill? |
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Definition
Algorithm development and optimization
pipeline development |
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Term
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Definition
| the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space. |
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Term
| DNA processing is becoming |
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Definition
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Definition
| Quantitative Insights Into Microbial Ecology |
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Term
| What computer is Bioinformatics done on most? |
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Definition
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Term
| Why is Linux and Mac OS better? |
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Definition
| It is based on Unix. Windows does not have this. |
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Term
| Why is a virtual machine useful? |
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Definition
| It makes it possible to run Linux on top of Windows |
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Term
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Definition
| Linear sequences of binary numbers |
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Term
| Biological data is often represented in what form? |
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Definition
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Term
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Definition
| Easier to transfer between programs |
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Definition
| Comma separated text files. |
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Term
| What is delimited text often used for? |
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Definition
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Term
| What makes a good text editor? |
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Definition
| Line numbers on the side. |
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Term
| What is the central Dogma of Molecular Biology |
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Definition
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Term
| What are the building blocks of DNA |
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Definition
| Phosphate group, Sugar; base; nucleotide |
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Term
| What is the difference between RNA and DNA |
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Definition
Uracil in RNA
Thymine in DNA |
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Term
| Remember the composition of DNA and RNA |
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Definition
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Term
| Which direction does DNA go |
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Definition
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Term
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Definition
| A structural protein; a large component of human skin |
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Term
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Definition
| a key enzyme in photosynthesis. |
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Term
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Definition
| a six protein complex responsible for that disease state associated with cholera |
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Term
| Green Fluorescent protein |
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Definition
| Jellyfish protein responsible for bio luminescence |
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Term
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Definition
| Technically, a sequence of symbols that can be interpreted as a message |
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Term
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Definition
| A bit, A byte, A kilobyte |
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Definition
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Definition
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Term
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Definition
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Term
| what do the numbers represent? 2^3 |
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Definition
2 stands for the 0 & 1
^3 stands for place holders in binary. |
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Term
| What are proteins made of? |
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Definition
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Term
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Definition
GC is stronger than AT
because of an additional Hydrogen bond |
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Term
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Definition
AT is weaker than GC
because of a lesser Hydrogen bond |
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Definition
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Definition
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Definition
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Definition
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Term
| What happens during transcription |
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Definition
RNA Polymerase reads the DNA's 3'to 5'
because RNA needs to be read in the 5'to3' |
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Term
| Aspects of an Evolutionary Process |
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Definition
Descent
Mutation
Variation
Selection
Drift |
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Term
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Definition
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Term
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Definition
| The composition of all that is in an animal. Somatic cells can not be used for mating |
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Term
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Definition
| The cells that are going to be involved in mating |
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Term
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Definition
| When new genes are derived from existing genes |
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Term
| What is a synonymous point mutation |
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Definition
The result of a mutation in the same amino acid sequence
CUU -> CUG (Still encodes for Leu |
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Term
| What is a non-synonymous point mutation |
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Definition
The result of a mutation in a different amino acid sequence
UUA -> UUU (Was Leu, it becomes Phe)
This will also happen for indels |
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Term
| What is an Insertion/Deletion (indels) mutation |
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Definition
A mutation as a result of a change in the reading frame.
This is a non-synonymous mutation |
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Term
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Definition
| The number of viable offspring produced |
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Term
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Definition
| Not all offspring reproduce equally |
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Term
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Definition
| random, but they can sometimes result in an adaptive change. |
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Term
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Definition
| Derived from the ancestral gene |
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Term
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Definition
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Term
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Definition
| The same gene, that is derived from a common ancestor. |
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Term
| What is a Needleman-Wunsch alignement |
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Definition
Two guys that worked on the algorithm
a way to get around the limitations we identified in scoring gaps in DNA strands equally. This solution is to discern the possibility that an amino acid is derived from a common ancestor |
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Term
| What does an alignment represent? |
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Definition
| A hypthesis about the evolutionary history of a sequence. Which of these hypothesis is more likely to be true based on what you know about sequence evolution? |
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Term
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Definition
| Taking a portion of sequences and aligning the particle sample. |
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Term
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Definition
| Taking two sequence and aligning the whole thing together |
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Term
| What is the Smith-Waterman Local sequence alignment |
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Definition
| an algorithm used for performing pairwise local alignment. It is nearly identical to Needleman-Wunsch, with three small important differences. |
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Term
| What is the difference in Smith-Waterman alignment |
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Definition
Difference: Initialization is easier.
F(0,0) = 0
F(i, 0) = 0
F(0, j) = 0 |
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Term
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Definition
Difference: One more additional term. A 0 is appended to the possible values. This allows for cells that do not appear at all when they have a negative score.
(Where a score is the most hypothetically optimal ancestral organism) |
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Term
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Definition
| Difference: You look for the highest score to find your local alignment, instead of going directly to the lower right corner. |
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Term
| What is phylogenetic reconstruction? |
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Definition
| The process of making inferences in the evolutionary relationships between organisms. |
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Term
| how are phylogenetic trees built |
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Definition
| Based on the traits that are collected from organisms. |
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Term
| What is pairwise sequence alignment? |
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Definition
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Term
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Definition
| Unweighted Pair Group Method with Arithmetic mean. |
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Term
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Definition
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Term
| What is the goal of building the tree? |
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Definition
| Getting pairwise alignments to work |
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Term
| What does the length mean in the tree? |
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Definition
| Represents the pairs of sequence that match. |
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Term
| What does a node in a tree represent? |
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Definition
| Signifies a common ancestor. |
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Term
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Definition
| doesn't include an assumption about the last common ancestor of all sequences |
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Term
| Terminal nodes, tips or leaves |
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Definition
| extant organisms, frequently called operational taxonomic units or OTUs. OTUs are families of related organisms. |
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Term
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Definition
| an internal node and all nodes "below" it (i.e., toward the tips) |
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Term
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Definition
| the internal node defining the clade which contains all nodes in the tree |
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Term
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Definition
| representative of the distance between the nodes. |
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Term
| What is a Monophyletic group |
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Definition
| the last common ancestor was a member of the group (e.g., multicellular organisms) |
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Term
| What is a Polyphyletic group |
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Definition
| the last common ancestor was not a member of the group (e.g., flying animals) |
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