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Glossary Molecular Biology and Computational Biology

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Backcross A cross between an animal that is heterozygous for alleles obtained from two parental strains and a second animal from one of those parental strains. Also used to describe the breeding protocol of an outcross followed by a backcross.

Bacterial artificial chromosome (BAC) A vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. Based on naturally occurring F-factor plasmid found in the bacterium E. coli.

Bacterial artificial chromosome (BAC) Large segments of DNA, 100,000 to 200,000 bases, from another species cloned into bacteria. Once the foreign DNA has been cloned into the host bacteria, many copies of it can be made. (NHGRI)

Bacteriophage Structures are usually closed by main-chain hydrogen bonds between the first and last strands of the beta sheet, in this case it is defined by the two integer numbers: the number of strand in the beta sheet, n, and a measure of the extent the extent to which the strands in the sheet are staggered the shear number, S. (SCOP)

Base One of the molecules that form DNA and RNA molecules.

Base pair (bp)/b> Two nitrogenous bases (adenine and thymine or guanine and cytosine) held together by weak bonds. Two strands of DNA are held together in the shape of a double helix by the bonds between base pairs. (ORNL)

Base sequence The order of nucleotide bases in a DNA molecule; determines structure of proteins encoded by that DNA. (ORNL)

Base sequence analysis A method, sometimes automated, for determining the base sequence. (ORNL)

Behavioral genetics The study of genes that may influence behavior. (ORNL)

Beta-sheet Can be antiparallel (i.e. the strand direction in any two adjacent strands are antiparallel), parallel (all strands are parallel each other) and mixed (there is one strand at least that is parallel to one of its two neighbours and antiparallel to the other). (SCOP)

Bioinformatics The merger of biotechnology and information technology with the goal of revealing new insights and principles in biology. (NCBI)

Bioinformatics The science of managing and analyzing biological data using advanced computing techniques. Especially important in analyzing genomic research data.

Bioremediation The use of biological organisms such as plants or microbes to aid in removing hazardous substances from an area. (ORNL)

Biotechnology A set of biological techniques developed through basic research and now applied to research and product development. In particular, biotechnology refers to the use by industry of recombinant DNA, cell fusion, and new bioprocessing techniques. (ORNL)

Birth defect Any harmful trait, physical or biochemical, present at birth, whether a result of a genetic mutation or some other nongenetic factor.

Bit score The value S' is derived from the raw alignment score S in which the statistical properties of the scoring system used have been taken into account. Because bit scores have been normalized with respect to the scoring system, they can be used to compare alignment scores from different searches. (NCBI)

Bits scores Alignment scores are reported by HMMer and BLAST as bits scores. The likelihood that the query sequence is a bona fide homologue of the database sequence is compared to the likelihood that the sequence was instead generated by a "random" model. Taking the logarithm (to base 2) of this likelihood ratio gives the bits score. (SMART)

BLAST Basic Local Alignment Search Tool. (Altschul et al.) A sequence comparison algorithm optimized for speed used to search sequence databases for optimal local alignments to a query. The initial search is done for a word of length "W" that scores at least "T" when compared to the query using a substitution matrix. Word hits are then extended in either direction in an attempt to generate an alignment with a score exceeding the threshold of "S". The "T" parameter dictates the speed and sensitivity of the search. For additional details, see one of the BLAST tutorials (Query or BLAST) or the narrative guide to BLAST. (NCBI)

BLAST A computer program that identifies homologous (similar) genes in different organisms, such as human, fruit fly, or nematode. (ORNL)

BLOSUM Blocks Substitution Matrix. A substitution matrix in which scores for each position are derived from observations of the frequencies of substitutions in blocks of local alignments in related proteins. Each matrix is tailored to a particular evolutionary distance. In the BLOSUM62 matrix, for example, the alignment from which scores were derived was created using sequences sharing no more than 62% identity. Sequences more identical than 62% are represented by a single sequence in the alignment so as to avoid over-weighting closely related family members. (Henikoff and Henikoff) (NCBI)

Bundle An array of alpha-helices each oriented roughly along the same (bundle) axis. It may have twist, left-handed if each helix makes a positive angle to the bundle axis, or, right-handed if each helix makes a negative angle to the bundle axis. (SCOP)

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