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BioJava is an open-source software project dedicated to provide Java tools to process biological data. [1] [2] [3] BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic ...
Similarly, the same sequences in the fugu genome have 68% identity to human UCEs, despite the human genome only reliably aligning to 1.8% of the fugu genome. [4] Despite often being noncoding DNA, [6] some ultraconserved elements have been found to be transcriptionally active, producing non-coding RNA molecules. [7]
In the shortest common supersequence problem, two sequences X and Y are given, and the task is to find a shortest possible common supersequence of these sequences. In general, an SCS is not unique. For two input sequences, an SCS can be formed from a longest common subsequence (LCS) easily.
In Java, lazy evaluation can be done by using objects that have a method to evaluate them when the value is needed. The body of this method must contain the code required to perform this evaluation. Since the introduction of lambda expressions in Java SE8, Java has supported a compact
The main non-scalar construct of SequenceL is the sequence, which is essentially a list. Sequences may be nested to any level. To avoid the routine use of recursion common in many purely functional languages, SequenceL uses a technique termed normalize–transpose (NT), in which scalar operations are automatically distributed over elements of a ...
In computer science, Hirschberg's algorithm, named after its inventor, Dan Hirschberg, is a dynamic programming algorithm that finds the optimal sequence alignment between two strings. Optimality is measured with the Levenshtein distance , defined to be the sum of the costs of insertions, replacements, deletions, and null actions needed to ...
Hotel Willa: Taos, New Mexico. Hotel Willa is set to open its doors in early 2025. Located in the Downtown Taos Historic District and overlooking the Couse pasture and Sangre de Cristo Mountains ...
UCbase is a database of ultraconserved sequences (UCRs or UCEs) that were first described by Bejerano, G. et al. [2] in 2004. They are highly conserved genome regions that share 100% identity among human, mouse and rat. UCRs are 481 sequences longer than 200 bases.