Bioinformatics Exam 1

Bioinformatics

Use of biology and computing to analyze biological data and extract meaningful information

Genomics

Study of complete genomes including their structure function variation and evolution

Genetics

Study of genes inheritance and individual traits

Genome

Complete genetic material of an organism

Genotype

Genetic information or genetic makeup of an organism

Transcriptome

Complete collection of RNA transcripts expressed in a cell or organism

Proteome

Complete set of proteins expressed by a cell or organism

Algorithm

Step-by-step procedure for solving a problem

Programming

Writing computer instructions to perform tasks

Python

Readable programming language used for scripting automation and biological data analysis

C

Compiled programming language useful for high-speed and memory-efficient analysis

C++

High-performance programming language used to develop computational tools

R

Programming language used for statistics and data visualization

Perl

Programming language historically used for biological sequence and text processing

Bash

Shell language used to run and automate command-line operations

Java

Programming language associated with graphical applications

HTML

Markup language used to structure web pages

Unix

Operating system widely used in scientific computing

Linux

Open-source Unix-like operating system

Sequence alignment

Arrangement of biological sequences to identify corresponding residues and similarities

Sequence identity

Exact matches at aligned positions

Sequence similarity

Resemblance between sequences including conservative amino acid substitutions

Homology

Evolutionary relationship due to common ancestry

Conserved region

Sequence region that remains similar across organisms or related sequences

Global alignment

Alignment across the full lengths of two sequences

Local alignment

Alignment of the highest-scoring matching regions within two sequences

Needleman-Wunsch

Dynamic programming algorithm for global sequence alignment

Smith-Waterman

Dynamic programming algorithm for local sequence alignment

Needle

Program for global sequence alignment using Needleman-Wunsch

Water

Program for local sequence alignment using Smith-Waterman

Gap

Space inserted in an alignment to represent a possible insertion or deletion

Indel

Insertion or deletion of sequence residues

Gap penalty

Score reduction used to discourage excessive gaps in an alignment

Dot plot

Graph comparing two sequences by marking positions where residues match

Dot plot diagonal

Pattern indicating similarity between sequences

Dot plot interrupted diagonal

Pattern suggesting an insertion or deletion

Dot plot parallel diagonals

Pattern suggesting repeated or duplicated sequence regions

Dot plot reverse diagonal

Pattern suggesting a possible inversion

Edit script

Series of operations that transforms one sequence into another

Hamming distance

Number of mismatched positions between equal-length strings

Levenshtein distance

Minimum number of insertions deletions and substitutions needed to transform one string into another

Alignment score

Numerical measure of alignment quality based on matches mismatches substitutions and gaps

Substitution matrix

Table assigning scores to amino acid matches and replacements

Positive substitution score

Amino acid substitution observed more frequently than expected by chance

Zero substitution score

Amino acid substitution occurring approximately as frequently as expected by chance

Negative substitution score

Amino acid substitution observed less frequently than expected by chance

PAM

Point Accepted Mutation matrix based on substitutions observed in closely related proteins

PAM1

Matrix representing approximately one accepted amino acid change per 100 residues

PAM250

Matrix extrapolated from PAM1 to model greater evolutionary divergence

PAM numbering

Higher PAM values represent greater modeled evolutionary distance

BLOSUM

BLOcks SUbstitution Matrix derived from conserved blocks of protein families

BLOSUM62

Common general-purpose protein substitution matrix

BLOSUM numbering

Lower BLOSUM values are used for more divergent proteins

Dynamic programming

Method that systematically finds optimal sequence alignments for a scoring system

Optimal alignment

Alignment with the highest score under a specified scoring system

Multiple sequence alignment

Alignment of three or more sequences to identify conserved positions and relationships

ClustalW

Program that progressively aligns sequences using a guide tree

Clustal Omega

Multiple sequence alignment program using progressive alignment approaches

Guide tree

Tree used to determine the order of sequences or groups in progressive alignment

Distance matrix

Table describing pairwise distances between sequences

MUSCLE

Program for multiple sequence alignment

MAFFT

Program for multiple sequence alignment

T-Coffee

Program for multiple sequence alignment

ProbCons

Probabilistic multiple sequence alignment program

BLAST

Basic Local Alignment Search Tool used to search sequence databases for local similarity

Heuristic algorithm

Fast search method that finds good matches without guaranteeing the mathematically optimal alignment

Query sequence

Sequence submitted to a database search

Target sequence

Database sequence compared with the query

BLAST hit

Database sequence producing an alignment with the query

blastn

Compares a nucleotide query against a nucleotide database

blastp

Compares a protein query against a protein database

blastx

Translates a nucleotide query and compares it against a protein database

tblastn

Compares a protein query against a translated nucleotide database

tblastx

Compares translated nucleotide query sequences against translated nucleotide database sequences

Reading frame

One way to divide a nucleotide sequence into consecutive codons

Six reading frames

Three possible reading frames on each of the two DNA strands

E-value

Expected number of random database matches with a score at least as high as the observed alignment

Low E-value

Indicates a match is less likely to occur by chance

Bit score

Normalized sequence alignment score where higher values indicate stronger alignments

Percent identity

Percentage of aligned positions with exactly matching residues

Query coverage

Percentage of the query sequence included in the alignment

Conservative substitution

Replacement of an amino acid with another having similar properties

GenBank

NCBI resource containing nucleotide sequences and related genetic information

NCBI

National Center for Biotechnology Information providing biological databases and analysis tools

Ensembl

Genome database and browser providing gene and genome annotations

UniProt

Database of protein sequences and functional annotations

Swiss-Prot

Reviewed and manually curated section of UniProtKB

TrEMBL

Unreviewed and computationally annotated section of UniProtKB

PDB

Protein Data Bank containing three-dimensional structures of biological macromolecules

PROSITE

Resource for identifying protein motifs signatures and functional sites

Pfam

Resource for protein families and domains

Pfam-A

Historically manually curated high-quality Pfam families

Pfam-B

Historical automatically generated lower-confidence Pfam families

InterPro

Resource integrating protein signatures to classify families domains and functional sites

Gene Ontology

Standard vocabulary for describing gene product functions processes and locations

Molecular function

Gene Ontology category describing what molecular activity a gene product performs

Biological process

Gene Ontology category describing larger biological pathways or processes

Cellular component

Gene Ontology category describing where a gene product functions

Protein domain

Distinct structural or functional region of a protein

Protein motif

Short recurring sequence or structural pattern associated with a function