SeqAn An efficient, generic C++ library for sequence analysis
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Summary
The design and content of SeqAn are described, which comprises implementations of existing, practical state-of-the-art algorithmic components to provide a sound basis for algorithm testing and development and greatly simplifies the rapid development of new bioinformatics tools.
- Type
- article
- Published
- 2008-01-09
- Cited by
- 381
- References
- 58
- Access
- Open access
- OpenAlex
- https://openalex.org/W2075996757
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:8244335
Keywords
Computer science, USable, Implementation, String searching algorithm, Sequence (biology)
References
- The sequence of the human genome. Venter JC,∗ Adams MD, Myers EW, et al. Science 2001;291:1304–1351.
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- Better Filtering with Gapped q-Grams
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- Generative Programming: Methods, Tools, and Applications
- A whole-genome assembly of Drosophila.
- libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny
- Suffix arrays: a new method for on-line string searches
- Efficient implementation of lazy suffix trees
- Mauve: multiple alignment of conserved genomic sequence with rearrangements.
- BioJava: open source components for bioinformatics
- Chaining multiple-alignment fragments in sub-quadratic time
- Generalized suffix trees for biological sequence data: applications and implementation
- q-gram based database searching using a suffix array (QUASAR)
- Basic local alignment search tool.
- An improved algorithm for matching biological sequences.
- A general method applicable to the search for similarities in the amino acid sequence of two proteins.
- Bio++: a set of C++ libraries for sequence analysis, phylogenetics, molecular evolution and population genetics
- The neighbor-joining method: a new method for reconstructing phylogenetic trees.
- A fast bit-vector algorithm for approximate string matching based on dynamic programming
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- Probabilistic Models for Collecting, Analyzing, and Modeling Expression Data
- Identification of Nutrient-Responsive Arabidopsis and Rapeseed MicroRNAs by Comprehensive Real-Time Polymerase Chain Reaction Profiling and Small RNA Sequencing1[C][W][OA]
- OpenMS and TOPP: Open Source Software for LC-MS Data Analysis
- Prospects and limitations of full-text index structures in genome analysis
- Determining the difficulty of Word Sense Disambiguation
- Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens
- The khmer software package: enabling efficient nucleotide sequence analysis
- Dynamic Gap Selector: A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimization
- Finding Optimal Sets of Enriched Regions in ChIP-Seq Data
- Assembly algorithms for next-generation sequence data
- Computational Methods for Personalized Cancer Therapy Based on Genomics Data
- Population Based Microsatellite Genotyping
- A General Paradigm for Fast, Adaptive Clustering of Biological Sequences
- Methods for High-Throughput Comparative genomics and Distributed sequence Analysis
- Genome-wide analysis of mutually exclusive splicing.
- PresCont: Vorhersage von Protein-Protein Interaktionsflächen unter Verwendung struktureller und evolutionärer Eigenschaften
- PopAlu: population-scale discovery of Alu polymorphisms
- Computational analysis of small RNAs and the RNA degradome with application to plant water stress
- Next-generation sequencing algorithms: from read mapping to variant detection
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