STELLAR: Fast and exact local alignments

BMC Bioinformatics

Volumn 12, Issue SUPPL. 9, 2011, Pages

  Kehr, Birte ^a,b   Weese, David ^a   Reinert, Knut ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b International Max Planck Research School for Computational Biology and Scientific Computing   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

C++ LIBRARIES; EDIT DISTANCE; GENOMIC SEQUENCE; LOCAL ALIGNMENT; LONG SEQUENCES; MAXIMAL ERROR; MINIMAL LENGTHS; VERIFICATION STRATEGY;

COMPUTER OPERATING SYSTEMS; COMPUTER SIMULATION; GENES; TOOLS;

STARS;

ALGORITHM; ANIMAL; ARTICLE; COMPUTER PROGRAM; DROSOPHILA; GENETICS; GENOMICS; METHODOLOGY; SEQUENCE ALIGNMENT;

ALGORITHMS; ANIMALS; DROSOPHILA; GENOMICS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 80053483140     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S9-S15     Document Type: Article

References (34)

1. Sellers PH. The theory and computation of evolutionary distances: Pattern recognition. Journal of Algorithms 1980, 1(4):359-373.
2. Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol 1981, 147:195-197. 10.1016/0022-2836(81)90087-5, 7265238.
3. Paten B, Herrero J, Beal K, Birney E. Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinformatics 2009, 25(3):295-301. 10.1093/bioinformatics/btn630, 19056777.
4. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010, 5(6):e11147. 10.1371/journal.pone.0011147, 2892488, 20593022.
5. Dubchak I, Poliakov A, Kislyuk A, Brudno M. Multiple whole-genome alignments without a reference organism. Genome Res 2009, 19(4):682-689. 10.1101/gr.081778.108, 2665786, 19176791.
6. Raphael B, Zhi D, Tang H, Pevzner P. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res 2004, 14(11):2336-2346. 10.1101/gr.2657504, 525693, 15520295.
7. Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004, 14(4):708-715. 10.1101/gr.1933104, 383317, 15060014.
8. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
9. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
10. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18(11):1851-1858. 10.1101/gr.078212.108, 2577856, 18714091.
11. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24(5):713-714. 10.1093/bioinformatics/btn025, 18227114.
12. Rumble S, Brudno M. Shrimp - short read mapping package. 2008, http://compbio.cs.toronto.edu/shrimp/
13. Jiang H, Wong WH. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 2008, 24(20):2395-2396. 10.1093/bioinformatics/btn429, 2562015, 18697769.
14. Weese D, Emde AK, Rausch T, Döring A, Reinert K. RazerS-fast read mapping with sensitivity control. Genome Res 2009, 19(9):1646-1654. 10.1101/gr.088823.108, 2752123, 19592482.
15. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628. 10.1038/nmeth.1226, 18516045.
16. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 1988, 85(8):2444-2448. 10.1073/pnas.85.8.2444, 280013, 3162770.
17. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
18. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
19. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol 2000, 7(1-2):203-214. 10.1089/10665270050081478, 10890397.
20. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664. 187518, 11932250.
21. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res 2003, 13:103-107. 10.1101/gr.809403, 430961, 12529312.
22. Lam TW, Sung WK, Tam SL, Wong CK, Yiu SM. Compressed indexing and local alignment of DNA. Bioinformatics 2008, 24(6):791-797. 10.1093/bioinformatics/btn032, 18227115.
23. Karlin S, Altschul SF. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A 1990, 87(6):2264-2268. 10.1073/pnas.87.6.2264, 53667, 2315319.
24. Döring A, Weese D, Rausch T, Reinert K. SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics 2008, 9:11. 10.1186/1471-2105-9-11, 2246154, 18184432.
25. Gogol-Döring A, Reinert K. Biological Sequence Analysis Using the SeqAn C++ Library. 2009, Chapman & Hall/CRC Mathematical & Computational Biology, CRC Press, Boca Raton, USA., http://www.crcpress.com/ecommerce_product/product_detail.jsf?isbn=9781420076233
26. Zhang Z, Berman P, Miller W. Alignments without low-scoring regions. J Comput Biol 1998, 5(2):197-210. 10.1089/cmb.1998.5.197, 9672828.
27. Zhang Z, Berman P, Wiehe T, Miller W. Post-processing long pairwise alignments. Bioinformatics 1999, 15(12):1012-1019. 10.1093/bioinformatics/15.12.1012, 10745991.
28. Rasmussen KR, Stoye J, Myers EW. Efficient q-gram filters for finding all ε-matches over a given length. J Comput Biol 2006, 13(2):296-308. 10.1089/cmb.2006.13.296, 16597241.
29. Burkhardt S, Crauser A, Ferragina P, Lenhof HP, Rivals E, Vingron M. q-gram based database searching using a suffix array (QUASAR). J Comput Biol, RECOMB '99 1999, 77-83.
30. Jokinen P, Ukkonen E. Two algorithms for approxmate string matching in static texts. Mathematical Foundations of Computer Science 1991, Volume 520 of Lect Notes Comput Sc 1991, 240-248., http://www.springerlink.com/content/p58155n8012x0477/
31. Waterman MS, Eggert M. A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J Mol Biol 1987, 197(4):723-728. 10.1016/0022-2836(87)90478-5, 2448477.
32. Marzal A, Vidal E. Computation of normalized edit distance and applications. IEEE T Pattern Anal 1993, 15:926-932.
33. Arslan AN, Eǧecioǧlu T. Efficient algorithms for normalized edit distance. Journal of Discrete Algorithms 2000, 1:3-20.
34. Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H, Consortium F. FlyBase: enhancing drosophila gene ontology annotations. Nucleic Acids Res 2009, 37(Database issue):D555-D559. 2686450, 18948289.