SOAP: short oligonucleotide alignment program. We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets.

References in zbMATH (referenced in 22 articles , 1 standard article )

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  1. Daykin, Jacqueline W.; Groult, Richard; Guesnet, Yannick; Lecroq, Thierry; Lefebvre, Arnaud; Léonard, Martine; Prieur-Gaston, Élise: A survey of string orderings and their application to the Burrows-Wheeler transform (2018)
  2. Daykin, Jacqueline W.; Watson, Bruce: Indeterminate string factorizations and degenerate text transformations (2017)
  3. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  4. Shomroni, Orr: Development of algorithms and next-generation sequencing data workflows for the analysis of gene regulatory networks (2017)
  5. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  6. Mathé, Ewy (ed.); Davis, Sean (ed.): Statistical genomics. Methods and protocols (2016)
  7. Barton, Carl; Flouri, Tomáš; Iliopoulos, Costas S.; Pissis, Solon P.: Global and local sequence alignment with a bounded number of gaps (2015)
  8. Barton, Carl; Iliopoulos, Costas S.; Lee, Inbok; Mouchard, Laurent; Park, Kunsoo; Pissis, Solon P.: Extending alignments with $k$-mismatches and $\ell$-gaps (2014)
  9. Gog, Simon; Karhu, Kalle; Kärkkäinen, Juha; Mäkinen, Veli; Välimäki, Niko: Multi-pattern matching with bidirectional indexes (2014)
  10. Rossell, David; Attolini, Camille Stephan-Otto; Kroiss, Manuel; Stöcker, Almond: Quantifying alternative splicing from paired-end RNA-sequencing data (2014)
  11. Daugelaite, Jurate; O’Driscoll, Aisling; Sleator, Roy D.: An overview of multiple sequence alignments and cloud computing in bioinformatics (2013)
  12. Cox, Anthony J.; Jakobi, Tobias; Rosone, Giovanna; Schulz-Trieglaff, Ole B.: Comparing DNA sequence collections by direct comparison of compressed text indexes (2012)
  13. Giancarlo, R.; Scaturro, D.; Utro, F.: Textual data compression in computational biology: algorithmic techniques (2012)
  14. Iliopoulos, Costas S.; Kourie, Derrick; Mouchard, Laurent; Musombuka, Themba K.; Pissis, Solon P.; de Ridder, Corne: An algorithm for mapping short reads to a dynamically changing genomic sequence (2012)
  15. Policriti, Alberto; Tomescu, Alexandru I.; Vezzi, Francesco: A randomized numerical aligner (rNA) (2012)
  16. Saeed, Fahad; Perez-Rathke, Alan; Gwarnicki, Jaroslaw; Berger-Wolf, Tanya; Khokhar, Ashfaq: A high performance multiple sequence alignment system for pyrosequencing reads from multiple reference genomes (2012) ioport
  17. Välimäki, Niko; Ladra, Susana; Mäkinen, Veli: Approximate all-pairs suffix/prefix overlaps (2012)
  18. Ji, Yuan; Xu, Yanxun; Zhang, Qiong; Tsui, Kam-Wah; Yuan, Yuan; Norris, Clift jun.; Liang, Shoudan; Liang, Han: BM-map: Bayesian mapping of multireads for next-generation sequencing data (2011)
  19. Noé, Laurent; G{^i}rdea, Marta; Kucherov, Gregory: Designing efficient spaced seeds for SOLiD read mapping (2010)
  20. Li, Ruiqiang; Yu, Chang; Li, Yingrui; Lam, Tak Wah; Yiu, Siu-Ming; Kristiansen, Karsten; Wang, Jun: SOAP2: an improved ultrafast tool for short read alignment (2009) ioport

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