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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 ...
A shortest common supersequence (SCS) is a common supersequence of minimal length. In the SCS 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
Software for ultra fast local DNA sequence motif search and pairwise alignment for NGS data (FASTA, FASTQ). DNA: Hepperle D (www.sequentix.de) 2020 Genoogle Genoogle uses indexing and parallel processing techniques for searching DNA and Proteins sequences. It is developed in Java and open source. Both: Albrecht F: 2015 HMMER
Apache Cayenne is an open source persistence framework licensed under the Apache License, providing object-relational mapping (ORM) and remoting services. Cayenne binds one or more database schemas directly to Java objects, managing atomic commit and rollbacks, SQL generation, joins, sequences, and more.
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]
The question of deciding which gap sequence to use is difficult. Every gap sequence that contains 1 yields a correct sort (as this makes the final pass an ordinary insertion sort); however, the properties of thus obtained versions of Shellsort may be very different. Too few gaps slows down the passes, and too many gaps produces an overhead.
In mathematics and computer science, Recamán's sequence [1] [2] is a well known sequence defined by a recurrence relation. Because its elements are related to the previous elements in a straightforward way, they are often defined using recursion .
[8] Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with restriction enzymes. Analyze sequences: find chimeras, [9] detect repeats, predict secondary structure, classify into a taxonomy of organisms [10] or functions, [11] create phylogenetic trees, and ancestral ...