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Number Cited by Other Article(s)
51
Laehnemann D, Borkhardt A, McHardy AC. Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction. Brief Bioinform 2016;17:154-79. [PMID: 26026159 PMCID: PMC4719071 DOI: 10.1093/bib/bbv029] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/09/2015] [Indexed: 12/23/2022]  Open
52
Pal S, Aluru S. In search of perfect reads. BMC Bioinformatics 2015;16 Suppl 17:S7. [PMID: 26679555 PMCID: PMC4674851 DOI: 10.1186/1471-2105-16-s17-s7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
53
Saha S, Rajasekaran S. EC: an efficient error correction algorithm for short reads. BMC Bioinformatics 2015;16 Suppl 17:S2. [PMID: 26678663 PMCID: PMC4674864 DOI: 10.1186/1471-2105-16-s17-s2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]  Open
54
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. Gigascience 2015;4:48. [PMID: 26500767 PMCID: PMC4615873 DOI: 10.1186/s13742-015-0089-y] [Citation(s) in RCA: 329] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022]  Open
55
Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. Nat Commun 2015;6:8212. [PMID: 26354079 PMCID: PMC4568561 DOI: 10.1038/ncomms9212] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 07/29/2015] [Indexed: 12/22/2022]  Open
56
Iyer S, Casey E, Bouzek H, Kim M, Deng W, Larsen BB, Zhao H, Bumgarner RE, Rolland M, Mullins JI. Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection. PLoS One 2015;10:e0135903. [PMID: 26317928 PMCID: PMC4552882 DOI: 10.1371/journal.pone.0135903] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 07/27/2015] [Indexed: 01/03/2023]  Open
57
Allam A, Kalnis P, Solovyev V. Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data. Bioinformatics 2015;31:3421-8. [DOI: 10.1093/bioinformatics/btv415] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 07/08/2015] [Indexed: 11/12/2022]  Open
58
Song L, Florea L, Langmead B. Lighter: fast and memory-efficient sequencing error correction without counting. Genome Biol 2015;15:509. [PMID: 25398208 PMCID: PMC4248469 DOI: 10.1186/s13059-014-0509-9] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/02/2023]  Open
59
Marçais G, Yorke JA, Zimin A. QuorUM: An Error Corrector for Illumina Reads. PLoS One 2015;10:e0130821. [PMID: 26083032 PMCID: PMC4471408 DOI: 10.1371/journal.pone.0130821] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 05/26/2015] [Indexed: 11/18/2022]  Open
60
Sheikhizadeh S, de Ridder D. ACE: accurate correction of errors usingK-mer tries. Bioinformatics 2015;31:3216-8. [DOI: 10.1093/bioinformatics/btv332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 05/22/2015] [Indexed: 11/13/2022]  Open
61
Craveiro SR, Inglis PW, Togawa RC, Grynberg P, Melo FL, Ribeiro ZMA, Ribeiro BM, Báo SN, Castro MEB. The genome sequence of Pseudoplusia includens single nucleopolyhedrovirus and an analysis of p26 gene evolution in the baculoviruses. BMC Genomics 2015;16:127. [PMID: 25765042 PMCID: PMC4346127 DOI: 10.1186/s12864-015-1323-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 02/04/2015] [Indexed: 11/10/2022]  Open
62
Salehi F, Baronio R, Idrogo-Lam R, Vu H, Hall LV, Kaiser P, Lathrop RH. CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generation sequencing. PLoS One 2015;10:e0116877. [PMID: 25692681 PMCID: PMC4333345 DOI: 10.1371/journal.pone.0116877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 12/08/2014] [Indexed: 01/12/2023]  Open
63
Schulz MH, Weese D, Holtgrewe M, Dimitrova V, Niu S, Reinert K, Richard H. Fiona: a parallel and automatic strategy for read error correction. ACTA ACUST UNITED AC 2015;30:i356-63. [PMID: 25161220 PMCID: PMC4147893 DOI: 10.1093/bioinformatics/btu440] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
64
Kopylova E, Noé L, Da Silva C, Berthelot JF, Alberti A, Aury JM, Touzet H. Deciphering metatranscriptomic data. Methods Mol Biol 2015;1269:279-91. [PMID: 25577385 DOI: 10.1007/978-1-4939-2291-8_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
65
Rare biosphere exploration using high-throughput sequencing: research progress and perspectives. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0678-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
66
Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D. GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers. PLoS One 2014;9:e107014. [PMID: 25198770 PMCID: PMC4157817 DOI: 10.1371/journal.pone.0107014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/07/2014] [Indexed: 12/28/2022]  Open
67
Ahola V, Lehtonen R, Somervuo P, Salmela L, Koskinen P, Rastas P, Välimäki N, Paulin L, Kvist J, Wahlberg N, Tanskanen J, Hornett EA, Ferguson LC, Luo S, Cao Z, de Jong MA, Duplouy A, Smolander OP, Vogel H, McCoy RC, Qian K, Chong WS, Zhang Q, Ahmad F, Haukka JK, Joshi A, Salojärvi J, Wheat CW, Grosse-Wilde E, Hughes D, Katainen R, Pitkänen E, Ylinen J, Waterhouse RM, Turunen M, Vähärautio A, Ojanen SP, Schulman AH, Taipale M, Lawson D, Ukkonen E, Mäkinen V, Goldsmith MR, Holm L, Auvinen P, Frilander MJ, Hanski I. The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nat Commun 2014;5:4737. [PMID: 25189940 PMCID: PMC4164777 DOI: 10.1038/ncomms5737] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/17/2014] [Indexed: 12/30/2022]  Open
68
Molnar M, Ilie L. Correcting Illumina data. Brief Bioinform 2014;16:588-99. [PMID: 25183248 DOI: 10.1093/bib/bbu029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/02/2014] [Indexed: 11/12/2022]  Open
69
Salmela L, Rivals E. LoRDEC: accurate and efficient long read error correction. ACTA ACUST UNITED AC 2014;30:3506-14. [PMID: 25165095 PMCID: PMC4253826 DOI: 10.1093/bioinformatics/btu538] [Citation(s) in RCA: 476] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
70
Lim EC, Müller J, Hagmann J, Henz SR, Kim ST, Weigel D. Trowel: a fast and accurate error correction module for Illumina sequencing reads. ACTA ACUST UNITED AC 2014;30:3264-5. [PMID: 25075116 DOI: 10.1093/bioinformatics/btu513] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
71
Greenfield P, Duesing K, Papanicolaou A, Bauer DC. Blue: correcting sequencing errors using consensus and context. ACTA ACUST UNITED AC 2014;30:2723-32. [PMID: 24919879 DOI: 10.1093/bioinformatics/btu368] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
72
Knief C. Analysis of plant microbe interactions in the era of next generation sequencing technologies. FRONTIERS IN PLANT SCIENCE 2014;5:216. [PMID: 24904612 PMCID: PMC4033234 DOI: 10.3389/fpls.2014.00216] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 04/30/2014] [Indexed: 05/18/2023]
73
Wirawan A, Harris RS, Liu Y, Schmidt B, Schröder J. HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC Bioinformatics 2014;15:131. [PMID: 24885381 PMCID: PMC4023493 DOI: 10.1186/1471-2105-15-131] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 04/24/2014] [Indexed: 01/29/2023]  Open
74
Alkio M, Jonas U, Declercq M, Van Nocker S, Knoche M. Transcriptional dynamics of the developing sweet cherry (Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes. HORTICULTURE RESEARCH 2014;1:11. [PMID: 26504533 PMCID: PMC4591669 DOI: 10.1038/hortres.2014.11] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 01/17/2014] [Indexed: 05/24/2023]
75
Mbandi SK, Hesse U, Rees DJG, Christoffels A. A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads. Front Genet 2014;5:17. [PMID: 24575122 PMCID: PMC3921913 DOI: 10.3389/fgene.2014.00017] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 01/19/2014] [Indexed: 11/13/2022]  Open
76
Istvánek J, Jaros M, Krenek A, Řepková J. Genome assembly and annotation for red clover (Trifolium pratense; Fabaceae). AMERICAN JOURNAL OF BOTANY 2014;101:327-37. [PMID: 24500806 DOI: 10.3732/ajb.1300340] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
77
Heo Y, Wu XL, Chen D, Ma J, Hwu WM. BLESS: bloom filter-based error correction solution for high-throughput sequencing reads. ACTA ACUST UNITED AC 2014;30:1354-62. [PMID: 24451628 DOI: 10.1093/bioinformatics/btu030] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
78
El-Metwally S, Ouda OM, Helmy M. Approaches and Challenges of Next-Generation Sequence Assembly Stages. NEXT GENERATION SEQUENCING TECHNOLOGIES AND CHALLENGES IN SEQUENCE ASSEMBLY 2014. [DOI: 10.1007/978-1-4939-0715-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
79
El-Metwally S, Hamza T, Zakaria M, Helmy M. Next-generation sequence assembly: four stages of data processing and computational challenges. PLoS Comput Biol 2013;9:e1003345. [PMID: 24348224 PMCID: PMC3861042 DOI: 10.1371/journal.pcbi.1003345] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
80
Ferrarini M, Moretto M, Ward JA, Šurbanovski N, Stevanović V, Giongo L, Viola R, Cavalieri D, Velasco R, Cestaro A, Sargent DJ. An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome. BMC Genomics 2013;14:670. [PMID: 24083400 PMCID: PMC3853357 DOI: 10.1186/1471-2164-14-670] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 09/26/2013] [Indexed: 11/10/2022]  Open
81
Iyer S, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI. Quality score based identification and correction of pyrosequencing errors. PLoS One 2013;8:e73015. [PMID: 24039850 PMCID: PMC3764156 DOI: 10.1371/journal.pone.0073015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 07/22/2013] [Indexed: 12/26/2022]  Open
82
Matullo G, Di Gaetano C, Guarrera S. Next generation sequencing and rare genetic variants: from human population studies to medical genetics. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2013;54:518-532. [PMID: 23922201 DOI: 10.1002/em.21799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 05/31/2013] [Accepted: 06/09/2013] [Indexed: 06/02/2023]
83
Deng W, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI. Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data. ACTA ACUST UNITED AC 2013;29:2402-9. [PMID: 23900188 DOI: 10.1093/bioinformatics/btt434] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
84
Ilie L, Molnar M. RACER: Rapid and accurate correction of errors in reads. ACTA ACUST UNITED AC 2013;29:2490-3. [PMID: 23853064 DOI: 10.1093/bioinformatics/btt407] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
85
Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z. Probabilistic error correction for RNA sequencing. Nucleic Acids Res 2013;41:e109. [PMID: 23558750 PMCID: PMC3664804 DOI: 10.1093/nar/gkt215] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
86
Nagarajan N, Pop M. Sequence assembly demystified. Nat Rev Genet 2013;14:157-67. [PMID: 23358380 DOI: 10.1038/nrg3367] [Citation(s) in RCA: 262] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
87
Liu Y, Schröder J, Schmidt B. Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. ACTA ACUST UNITED AC 2012. [PMID: 23202746 DOI: 10.1093/bioinformatics/bts690] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
88
Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson RH. Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets. Res Microbiol 2012;163:407-12. [PMID: 22824070 DOI: 10.1016/j.resmic.2012.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 06/26/2012] [Indexed: 12/31/2022]
89
Skums P, Dimitrova Z, Campo DS, Vaughan G, Rossi L, Forbi JC, Yokosawa J, Zelikovsky A, Khudyakov Y. Efficient error correction for next-generation sequencing of viral amplicons. BMC Bioinformatics 2012;13 Suppl 10:S6. [PMID: 22759430 PMCID: PMC3382444 DOI: 10.1186/1471-2105-13-s10-s6] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
90
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 2012;7:e37135. [PMID: 22675423 PMCID: PMC3365034 DOI: 10.1371/journal.pone.0037135] [Citation(s) in RCA: 2086] [Impact Index Per Article: 160.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 04/13/2012] [Indexed: 12/14/2022]  Open
91
Yang X, Chockalingam SP, Aluru S. A survey of error-correction methods for next-generation sequencing. Brief Bioinform 2012;14:56-66. [DOI: 10.1093/bib/bbs015] [Citation(s) in RCA: 177] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
92
Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A, Robertson DL. Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinformatics 2012;13:47. [PMID: 22443413 PMCID: PMC3359224 DOI: 10.1186/1471-2105-13-47] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 03/23/2012] [Indexed: 01/23/2023]  Open
93
Studholme DJ. Deep sequencing of small RNAs in plants: applied bioinformatics. Brief Funct Genomics 2011;11:71-85. [PMID: 22184332 DOI: 10.1093/bfgp/elr039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
94
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PLoS One 2011;6:e22594. [PMID: 21949676 PMCID: PMC3174933 DOI: 10.1371/journal.pone.0022594] [Citation(s) in RCA: 441] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 06/29/2011] [Indexed: 01/15/2023]  Open
95
Philippe N, Salson M, Lecroq T, Léonard M, Commes T, Rivals E. Querying large read collections in main memory: a versatile data structure. BMC Bioinformatics 2011;12:242. [PMID: 21682852 PMCID: PMC3163563 DOI: 10.1186/1471-2105-12-242] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 06/17/2011] [Indexed: 11/10/2022]  Open
96
Ranwez V, Harispe S, Delsuc F, Douzery EJP. MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PLoS One 2011. [PMID: 21949676 DOI: 10.1371/journal.pone.00022594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]  Open
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