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Repeated sequences (also known as repetitive elements, repeating units or repeats) are short or long patterns that occur in multiple copies throughout the genome. In many organisms, a significant fraction of the genomic DNA is repetitive, with over two-thirds of the sequence consisting of repetitive elements in humans. [ 1 ]
The ORF Finder (Open Reading Frame Finder) [15] is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database. This tool identifies all open reading frames using the standard or alternative genetic codes. The deduced amino acid sequence can be saved in ...
Sequence alignment. In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. [1] Aligned sequences of nucleotide or amino acid residues are typically represented ...
Bioinformatics tools aid in comparing, analyzing and interpreting genetic and genomic data and more generally in the understanding of evolutionary aspects of molecular biology. At a more integrative level, it helps analyze and catalogue the biological pathways and networks that are an important part of systems biology.
e. String functions are used in computer programming languages to manipulate a string or query information about a string (some do both). Most programming languages that have a string datatype will have some string functions although there may be other low-level ways within each language to handle strings directly.
The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims "to build a comprehensive parts list of functional elements in the human genome." [2]ENCODE also supports further biomedical research by "generating community resources of genomics data, software, tools and methods for genomics data analysis, and products resulting from data analyses and interpretations."
Aho–Corasick algorithm. In computer science, the Aho–Corasick algorithm is a string-searching algorithm invented by Alfred V. Aho and Margaret J. Corasick in 1975. [1] It is a kind of dictionary-matching algorithm that locates elements of a finite set of strings (the "dictionary") within an input text. It matches all strings simultaneously.
In computer science, an in-place algorithm is an algorithm that operates directly on the input data structure without requiring extra space proportional to the input size. In other words, it modifies the input in place, without creating a separate copy of the data structure. An algorithm which is not in-place is sometimes called not-in-place or ...