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Bioinformatics Final
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57
Microbiology
Undergraduate 4
12/08/2014

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Term
Three major DNA databases
Definition
EMBL
GenBank
DDBJ
Term
Flat-file database
Definition
Simplest form of a database. Information such as nucleotide or aa sequences are stored as either a large single text file or a collection of different text files
Term
Accession number
Definition
Label used to identify a sequence.
Ex: X102275 GenBank Genomic DNA sequence DNA
Term
FastA
Definition
Simple sequence format used in flat-file databases
Ex: Header line for DNA
sequence
Term
PDB
Definition
File format for 3D structures like proteins
Term
Structured Query Language
Definition
Computer language used with relational databases
Term
INDEL
Definition
Insertion or deletion mutations
Term
Block
Definition
Highly conserved local regions of DNA that are used in BLOSUM substitution matrices
Term
Multiple Sequence Alignment
Definition
Collection of three or more sequences that are partially or completely aligned. Residues are inferred to be homologous
Term
Feng-Doolittle
Definition
Method of constructing MSAs
Term
BLAST steps
Definition
1:Compile a list of words
2:Scan the database for entries that match the compiled list
3:When a hit on a word pair is found, the hit is extended in either direction until the score drops below a certain cutoff
Term
Psi-BLAST
Definition
Position-specific iterated BLAST that iteratively searches a protein sequence database, using the matches in round I to construct a PSSM for searching the database
Term
Delta-BLAST
Definition
Searches a database of pre-constructed PSSMs before searching a protein database to yield better homology detection.
Term
HMM
Definition
Hidden Markov Model
Term
Pfam
Definition
Database with a large collection of protein families, each represented by multiple sequence alignments (MSAs) and Hidden Markov Models (HMMs)
Term
Profile Hidden Markov Model
Definition
Can represent a sequence alignment profile similar to how a PSSM (position-specific scoring matrix) does.

A profile HMM includes information on amino acid consensus at each position in the alignment like a PSSM.

A profile HMM also has position-specific scores for gap insertions and deletions
Term
Things needed to build an HMM
Definition
Need to determine two things
1: structure/topology of the HMM-states and transitions.
2: The values of the parameters-emission and transition probablities
Term
How to build an HMM
Definition
1: Pick HMM structure/topology
2: Estimate initial parameters
3: Train the HMM by running sequences through it
4: Transitions that get used are given higher probabilities, those rarely used are given lower probabilities
Term
Databases that use HMMs
Definition
Pfam & SMART
Term
Unrooted tree
Definition
Fully resolved phylogenetic tree with each node connecting ancestors and descendants, but direction of evolution (which ancestor evolved from which) is undetermined
Term
Rooted tree
Definition
Phylogenetic tree in which one species is designated as the "root", the last common ancestor of all species below it
Term
Internal nodes
Definition
Represent hypothetical ancestors of taxa
Term
Terminal nodes
Definition
Represent the taxa (genes, proteins, species) used to infer the phylogeny
Term
Cladogram
Definition
Branch lengths have no meaning
Term
Additive tree
Definition
Branch lengths are a measure of evolutionary divergence
Term
Ultrametric tree
Definition
Branch lengths are a measure of evolutionary divergence
Same constant rate of mutation assumed along all branches
Term
Ortholog
Definition
Genes in different species that evolved from a common ancestral gene. Possess the same function
Term
Paralog
Definition
Genes in the same species that evolved from a common ancestral gene and created by gene duplication. Develop different functions, though often related to old funtions
Term
What can be learned from character analysis using phylogenies?
Definition
When did specific episodes of positive Darwinian selection occur during evolutionary history?

Which genetic changes are unique to the human lineage?

What was the most likely geographical location of the common ancestor of the African apes and humans?
Term
Bootstrap Procedure
Definition
Assigns values to individual branches that indicate the percentage occurrence
Term
Consensus tree
Definition
Shows only features that are consistent between multiple possible trees
Term
P-distance
Definition
This distance is the proportion (p) of nucleotide sites at which two sequences being compared are different. It is obtained by dividing the number of nucleotide differences by the total number of nucleotides compared.
Term
Transition
Definition
Changing purine to purine, or pyrimidine to pyrimidine
More common than transversion
Term
Transversion
Definition
Changing purine to pyrimidine, or pyrimidine to purine
Less common that transition
Term
Positive selection
Definition
Greater # of non-synonymous mutations observed than expected, indicates that mutations are more likely to be retained
Term
Negative selection
Definition
Smaller # of non-synonymous mutations observed than expected, indicates that mutations are being selected against and the sequence is conserved
Term
COGs
Definition
Clusters of Orthologous Genes
Used to find paralogs and homologs.
All genes in a species genome are compared against each other and against all genes in another species. If a gene's best-scoring BLAST hit (BeT) is within the genome, they are paralogs. If they BeT is between species, the genes are homologs.
Term
DSSP
Definition
Method for the assignment of secondary structure in a protein, uses hydrogen bond patterns
Term
STRIDE
Definition
Method for the assignment of secondary structure in a protein, uses both hydrogen bond energy and backbone dihedral angles
Term
DEFINE
Definition
Method for the assignment of secondary structure in a protein, matches the interatomic distances within the protein to those from idealized secondary structures.
Term
1st method of protein attachment to membrane
Definition
Attachment due to ionic interactions between protein and cytosolic face of the lipid bilayer
Term
2nd method of protein attachment to membrane
Definition
Attachment via an anchor such as a lipid. Added to the protein post-translationally, meaning that these types of proteins have no specialized structural or sequence features that can be identified
Term
3rd method of protein attachment to membrane
Definition
Bitopic membrane protein, in which the protein chain crosses the membrane exactly once
Term
4th method of protein attachment to membrane
Definition
Polytopic membrane protein, in which the protein chain threads back and forth across the membrane multiple times.
Term
X-ray crystallography
Definition
Used to determine most protein structures, requires crystals with a high protein concentration
Term
NMR
Definition
Used to determine some protein structures. Limited to smaller proteins
Term
Threading method
Definition
Method of predicting protein structure by using a library of folds and comparing the energies of different folds for the target sequence. These folds are then scored and the best-scoring ones are used in the model.
Term
Homology Method
Definition
Based on the assumption that homologous proteins have similar structures. Uses structure of known homologue to model target protein. More closely related sequences give better models.
Term
What do structurally reliable alignments depend on?
Definition
Sequence identity and alignment length
Term
SCR
Definition
Structurally Conserved Region
Term
Swiss Model
Definition
Automated protein structure homology-modeling server, used to model protein structures.
Term
Pearson Correlation Coefficient
Definition
Simple and fundamental method used to cluster microarray data.
Term
SOM
Definition
Self-organizing map.
Term
2D gel
Definition
Separates proteins based on both pH and size.
Term
BIND
Definition
Database of components and interactions, where each interaction includes information on cellular location, experimental conditions, conserved sequence, molecular location of interaction, and so on.
Term
KEGG Pathway
Definition
Draft metabolic reconstructions
Term
Steps in making KEGG Pathway
Definition
1.Draft reconstruction of metabolic network
2.Curate the reconstruction (add and correct information)
3.Convert to a computable metabolic model.
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