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Glossary
•
Agroinformatics / Agricultural informatics:
Agroinformatics concentrates on the aspects of bioinformatics dealing with plant genomes.•
Alignment
:The process of lining up two or moresequences to achieve maximal levels of identity(andconservation, in the case of amino acid sequences) for the purpose of assessing the degree of similarity andthe possibility of homology.
 Arrangement of two or morenucleotides of protein sequences to maximize thenumber of matching monomers
.•
Alignment score:
A numerical value that describes thequality of a sequence alignment.•
Algorithm
:A fixed procedure embodied in a computer program. A set of rules for calculating or problemsolving carried out by a computer program.•
Bioinformatics
:The merger of biotechnology andinformation technology with the goal of revealing newinsights and principles in biology.
 
 
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Annotation:
1-Finding genes and other importantelements in raw sequence data (structural annotation).2-Determining the function of genes and proteins(functional annotation)•
BLAST
 
B
asic
L
ocal
A
lignment
S
earch
T
ool. (Altschulet al.) A sequence comparisonalgorithmoptimized for  speed used to search sequence databases for optimallocal alignments to a query. The initial search is done for a word of length "W" that scores at least "T" whencompared to the query using a substitution matrix. Wordhits are then extended in either direction in an attempt togenerate an alignment with a score exceeding thethreshold of "S". The "T" parameter dictates the speedand sensitivity of the search.•
Database:
On a computer, a collection of data recordseither in a single file or as a multiple files. The centralcomponent of a database management system.
 
 
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Database management system (DBMS):
A software suite including adatabase and utilities required to organize, search, and update it, maintaindata security and control access.•
Domain:
Usually used to describe part of a protein that can fold and carryout a function independently, but sometimes used more generally to indicatepart of a protein sequence, for instance a ‘glycine-rich domain’, or ageometrically distinct part of a protein structure.•
E value
Expectation value used to test the significance of a sequencesimilarity score. The number of different alignents with scores equivalent toor better than S that are expected to occur in a database search by chance.The lower the E value, the more significant the score.•
FASTA
The first widely used algorithm (a sequence alignment algorithm) for database similarity searching. The program looks for optimal localalignments by scanning the sequence for small matches called "words".Initially, the scores of segments in which there are multiple word hits arecalculated ("init1"). Later the scores of several segments may be summed togenerate an "initn" score. An optimized alignment that includes gaps isshown in the output as "opt". The sensitivity and speed of the search areinversely related and controlled by the "k-tup" variable which specifies thesize of a "word". (Pearson and Lipman)
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