Quick Reference to Bioinformatics Vocabulary

This web page was produced as an assignment for bioinformatics at Samford University. 

A:

  • Alignment– The arrangement of two or more amino acid or base sequence from an organism or organisms in a fashion as to align the areas of the sequence that share common features. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This information can serve as a potential indicator of the genetic relatedness between the organisms.
  • Amino acid- The basic building blocks of proteins.

B:

  • Bases-  the components of DNA and RNA. There are four bases in DNA: adenine, guanine, cytosine, and thymine. (A,G,C,T). RNA replaces the thymine with uracil (U).
  • Base Pairs- pairing in DNA and RNA is specific between bases. Unless a mutation occurs, in DNA, Adenine pairs with Thymine, and Guanine pairs with Cytosine. However, in RNA Adenine pairs with Uracil.
  • Biology- the study of life or living matter in all its forms and phenomena, especially dealing with origin, growth, reproduction, structure, and behavior.
  • BLAST-  stands for Basic Local Alignment Search Tool. It specifically finds regions of local similarity between sequences. These sequences can be DNA, RNA, or amino acid sequences.The program compares the sequences to databases and calculates the statistical significance of matches.

C:

  • Computer Science-the science that deals with the theory and methods of processing information in digital computers, the design of computer software and hardware, and the applications of computers.

D:

  • Database- a comprehensive collection of related data organized for convenient access, generally in a computer.
  • DNA- stands for DeoxyriboNucleic Acid. Made up of nitrogenous bases (C, G, A, T),
  • Dot Plot- a visual tool to analyze two sequences to determine matches or regions of commonality between the two sequences.

E:

F:

G:

  • Gap- a place in a sequenced gene where there is discrepancies of what base pair(s) occur there. Also in aligned sequences, places in the aligned genes where there is no matches between all of them.
  • Gene-the basic physical unit of heredity; a linear sequence of nucleotides along a segment of DNA that provides the coded instructions for synthesis of RNA, which, when translated into protein, leads to the expression of hereditary character.
  • Genome-a full set of chromosomes; all the inheritable traits of an organism.
  • Genomics- the study of genomes.

H:

I:

  • Inversion- a mutation that can occur where a piece of the sequence has been flipped and reads backwards from the original sequence

J:

  • JASPAR- high quality transcription factor binding database

K:

L:

M:

  • Mismatch Limit-determines how similar the two sequences in a window must be to “match”. For example, if window size is 9 and mismatch limit is 2, then up to 2 mismatches in a 9 base window will still be classified as a match.
  • Mutations- a change in the sequencing of a gene. Can be large scale or a single change in base pairs. It is possible to have a mutation that does not manifest itself as well.

N:

O:

P:

  • Pathology- the study of diseases
  • Personalized Medicine- a type of medicine where a doctor has the entire genome of the patients, and through analysis of the genome, predictions about the possible diseases, predispositions, mutations, or disorders an individual might have. This is a hope for bioinformatics enthusiasts for the future of medicine.
  • Proteomics-  large scale study of proteins and their structure and function

Q:

R:

  • RNA- stands for ribo-nucleic acid. RNA is the material transcribed from DNA that is used to make proteins.

S:

  • Sequence- the arrangement or order of nucleotides or amino acids which corresponds to a piece of biological information (protein, gene, etc.)
  • Substitution Matrix-  describes therate at which one character in a sequence changes to other character states over time. Substitution matrices are usually seen in the context of amino acid or DNA sequence alignments, wherethe similarity between sequences depends on their divergence time and the substitution rates as represented in the matrix.

T:

U:

V:

W:

  • Window size-  number of bases in a sliding window that is moved along each sequence and compared to generate a single data point on the dot plot.

X:

Y:

Z:

References:

Dictionary.com. Dictionary.com. Web. 11 May 2012. <http://dictionary.reference.com/&gt;.

“Nucleic Acid Dot Plots.” Arbl.cvmbs.colostate.edu. Colorado State University. Web. 2 Apr. 2012. <http://www.vivo.colostate.edu/molkit/dnadot/&gt;

March 5, 2012

Jfleming@samford.edu

BIO 306

Samford University

Leave a comment