CSA: Agricultural Sample Survey for 2012/13. 2013, Ethiopia: Statistical Bulletin Addis Ababa
Google Scholar
Umeta M, West CE, Fufa H: Content of zinc, iron, calcium and their absorption inhibitors in foods commonly consumed in Ethiopia. J Food Compos Anal. 2005, 18 (8): 803-817.
CAS
Google Scholar
Eragrain. [http://www.eragrain.com/pdf/Consumer%20brochure%205-2012%20no%20address%20label.pdf]
Alaunyte I, Stojceska V, Plunkett A, Ainsworth P, Derbyshire E: Improving the quality of nutrient-rich Teff (Eragrostis tef) breads by combination of enzymes in straight dough and sourdough breadmaking. J Cereal Sci. 2012, 55 (1): 22-30.
CAS
Google Scholar
Tye-Din JA, Stewart JA, Dromey JA, Beissbarth T, van Heel DA, Tatham A, Henderson K, Mannering SI, Gianfrani C, Jewell DP, Hill AV, McCluskey J, Rossjohn J, Anderson RP: Comprehensive, quantitative mapping of T cell epitopes in gluten in celiac disease. Sci Transl Med. 2010, 2 (41): 41ra51-
PubMed
Google Scholar
Hopman E, Dekking L, Blokland ML, Wuisman M, Zuijderduin W, Koning F, Schweizer J: Tef in the diet of celiac patients in The Netherlands. Scand J Gastroenterol. 2008, 43 (3): 277-282.
CAS
PubMed
Google Scholar
Spaenij-Dekking L, Kooy-Winkelaar Y, Koning F: The Ethiopian cereal tef in celiac disease. New Engl J Med. 2005, 353 (16): 1748-1749.
CAS
PubMed
Google Scholar
Zeid M, Belay G, Mulkey S, Poland J, Sorrells ME: QTL mapping for yield and lodging resistance in an enhanced SSR-based map for tef. Theor Appl Genet. 2011, 122 (1): 77-93.
CAS
PubMed
Google Scholar
Yu JK, Sun Q, Rota ML, Edwards H, Tefera H, Sorrells ME: Expressed sequence tag analysis in tef (Eragrostis tef (Zucc) Trotter). Genome. 2006, 49 (4): 365-372.
CAS
PubMed
Google Scholar
Smith SM, Yuan YN, Doust AN, Bennetzen JL: Haplotype analysis and linkage disequilibrium at five loci in eragrostis tef. G3-Genes Genom Genet. 2012, 2 (3): 407-419.
CAS
Google Scholar
Ingram AL, Doyle JJ: The origin and evolution of Eragrostis tef (Poaceae) and related polyploids: Evidence from nuclear waxy and plastid rps16. Am J Bot. 2003, 90 (1): 116-122.
CAS
PubMed
Google Scholar
Bekele E, Lester RN: Biochemical assessment of the relationships of eragrostis-Tef (Zucc) Trotter with Some Wild Eragrostis Species (Gramineae). Ann Bot-London. 1981, 48 (5): 717-725.
CAS
Google Scholar
Hundera F, Arumuganathan K, Baenziger P: Determination of relative nuclear DNA content of tef [Eragrostis tef (Zucc.) Trotter] using flow cytometry. J Genet Breed. 2000, 54: 165-168.
Google Scholar
Soltis PS, Soltis DE: The role of hybridization in plant speciation. Annu Rev Plant Biol. 2009, 60: 561-588.
CAS
PubMed
Google Scholar
Van de Peer Y, Maere S, Meyer A: OPINION The evolutionary significance of ancient genome duplications. Nat Rev Genet. 2009, 10 (10): 725-732.
CAS
PubMed
Google Scholar
Brochmann C, Brysting AK, Alsos IG, Borgen L, Grundt HH, Scheen AC, Elven R: Polyploidy in arctic plants. Biol J Linn Soc. 2004, 82 (4): 521-536.
Google Scholar
Leitch AR, Leitch IJ: Perspective - genomic plasticity and the diversity of polyploid plants. Science. 2008, 320 (5875): 481-483.
CAS
PubMed
Google Scholar
Schatz MC, Witkowski J, McCombie WR: Current challenges in de novo plant genome sequencing and assembly. Genome Biol. 2012, 13 (4): 243-
CAS
PubMed Central
PubMed
Google Scholar
Phillippy AM, Schatz MC, Pop M: Genome assembly forensics: finding the elusive mis-assembly. Genome Biol. 2008, 9 (3): R55-
PubMed Central
PubMed
Google Scholar
Kelley DR, Salzberg SL: Detection and correction of false segmental duplications caused by genome mis-assembly. Genome Biol. 2010, 11 (3): R28-
PubMed Central
PubMed
Google Scholar
Yukawa M, Tsudzuki T, Sugiura M: The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum. Mol Genet Genomics. 2006, 275 (4): 367-373.
CAS
PubMed
Google Scholar
Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, Shang H, Zhu S, Zou C, Li Q, Yuan Y, Lu C, Wei H, Gou C, Zheng Z, Yin Y, Zhang X, Liu K, Wang B, Song C, Shi N, Kohel RJ, Percy RG, Yu JZ, Zhu YX, Wang J, Yu S: The draft genome of a diploid cotton Gossypium raimondii. Nat Genet. 2012, 44 (10): 1098-1103.
CAS
PubMed
Google Scholar
Wurm Y, Wang J, Riba-Grognuz O, Corona M, Nygaard S, Hunt BG, Ingram KK, Falquet L, Nipitwattanaphon M, Gotzek D, Dijkstra MB, Oettler J, Comtesse F, Shih CJ, Wu WJ, Yang CC, Thomas J, Beaudoing E, Pradervand S, Flegel V, Cook ED, Fabbretti R, Stockinger H, Long L, Farmerie WG, Oakey J, Boomsma JJ, Pamilo P, Yi SV, Heinze J, et al: The genome of the fire ant Solenopsis invicta. Proc Natl Acad Sci U S A. 2011, 108 (14): 5679-5684.
CAS
PubMed Central
PubMed
Google Scholar
Consortium PGS: Genome sequence and analysis of the tuber crop potato. Nature. 2011, 475 (7355): U189-U194.
Google Scholar
Schreiber AW, Hayden MJ, Forrest KL, Kong SL, Langridge P, Baumann U: Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat. BMC Genomics. 2012, 13: 492-
CAS
PubMed Central
PubMed
Google Scholar
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2011, 1 (1): 18-18.
Google Scholar
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al: Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005, 437 (7057): 376-380.
CAS
PubMed Central
PubMed
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011, 29 (7): 644-652.
CAS
PubMed Central
PubMed
Google Scholar
Zerbino DR, Birney E: Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18 (5): 821-829.
CAS
PubMed Central
PubMed
Google Scholar
Nakasugi K, Crowhurst R, Bally J, Waterhouse P: Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant nicotiana benthamiana. PLoS ONE. 2014, 9 (3): e91776-doi:10.1371/journal.pone.0091776
PubMed Central
PubMed
Google Scholar
Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye CY, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, et al: Reference genome sequence of the model plant Setaria. Nat Biotechnol. 2012, 30 (6): 555-561.
CAS
PubMed
Google Scholar
Zhang G, Liu X, Quan Z, Cheng S, Xu X, Xie M, Zeng P, Yue Z, Wang W, Tao Y, Bian C, Han C, Xia Q, Peng X, Cao R, Yang X, Zhan D, Hu J, Zhang Y, Li H, Li H, Li N, Wang J, Wang C, Wang R, Guo T, Cai Y, Liu C, Xiang H, Shi Q, et al: Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol. 2012, 30 (6): 549-554.
CAS
PubMed
Google Scholar
Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, Ren Y, Zhu H, Li J, Lin K, Jin W, Fei Z, Li G, Staub J, Kilian A, van der Vossen EA, Wu Y, Guo J, He J, Jia Z, Ren Y, Tian G, Lu Y, Ruan J, Qian W, Wang M, et al: The genome of the cucumber, cucumis sativus L. Nat Genet. 2009, 41 (12): 1275-1281.
CAS
PubMed
Google Scholar
Guo S, Zhang J, Sun H, Salse J, Lucas WJ, Zhang H, Zheng Y, Mao L, Ren Y, Wang Z, Min J, Guo X, Murat F, Ham BK, Zhang Z, Gao S, Huang M, Xu Y, Zhong S, Bombarely A, Mueller LA, Zhao H, He H, Zhang Y, Zhang Z, Huang S, Tan T, Pang E, Lin K, Hu Q, et al: The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet. 2012, 45 (1): 51-58.
PubMed
Google Scholar
Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JSS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Berard A, et al: The genome of Theobroma cacao. Nat Genet. 2010, 43 (2): 101-108.
PubMed
Google Scholar
Al-Mssallem IS, Hu S, Zhang X, Lin Q, Liu W, Tan J, Yu X, Liu J, Pan L, Zhang T, Yin Y, Xin C, Wu H, Zhang G, Ba Abdullah MM, Huang D, Fang Y, Alnakhli YO, Jia S, Yin A, Alhuzimi EM, Alsaihati BA, Al-Owayyed SA, Zhao D, Zhang S, Al-Otaibi NA, Sun G, Majrashi MA, Li F, Tala : De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol. 2011, 29 (6): 521-527.
Google Scholar
Marcais G, Kingsford C: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics. 2011, 27 (6): 764-770.
CAS
PubMed Central
PubMed
Google Scholar
Li XM, Waterman MS: Estimating the repeat structure and length of DNA sequences using l-tuples. Genome Res. 2003, 13 (8): 1916-1922.
CAS
PubMed Central
PubMed
Google Scholar
Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, et al: The sequence and de novo assembly of the giant panda genome (vol 463, pg 311, 2010). Nature. 2010, 463 (7284): 1106-1106.
CAS
Google Scholar
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, et al: The Sorghum bicolor genome and the diversification of grasses. Nature. 2009, 457 (7229): 551-556.
CAS
PubMed
Google Scholar
Holt C, Yandell M: MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics. 2011, 12 (1): 491-doi:10.1186/1471-2105-12-491
PubMed Central
PubMed
Google Scholar
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sanchez Alvarado A, Yandell M: MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008, 18 (1): 188-196.
CAS
PubMed Central
PubMed
Google Scholar
Lyons E, Freeling M: How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J. 2008, 53 (4): 661-673.
CAS
PubMed
Google Scholar
Lyons E, Pedersen B, Kane J, Freeling M: The value of nonmodel genomes and an example using SynMap Within CoGe to dissect the hexaploidy that predates the rosids. Trop Plant Biol. 2008, 1 (3–4): 181-190.
CAS
Google Scholar
Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M: Finding and comparing syntenic regions among arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol. 2008, 148 (4): 1772-1781.
CAS
PubMed Central
PubMed
Google Scholar
Krumsiek J, Arnold R, Rattei T: Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics. 2007, 23 (8): 1026-1028.
CAS
PubMed
Google Scholar
Zeid M, Belay G, Mulkey S, Poland J, Sorrells ME: QTL mapping for yield and lodging resistance in an enhanced SSR-based map for tef. Theor Appl Genet. 2010, 122 (1): 77-93.
PubMed
Google Scholar
Yang Z: PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007, 24 (8): 1586-1591.
CAS
PubMed
Google Scholar
Gaut BS, Morton BR, McCaig BC, Clegg MT: Substitution rate comparisons between grasses and palms: Synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci U S A. 1996, 93 (19): 10274-10279.
CAS
PubMed Central
PubMed
Google Scholar
Swigonova Z, Lai JS, Ma JX, Ramakrishna W, Llaca V, Bennetzen JL, Messing J: Close split of sorghum and maize genome progenitors. Genome Res. 2004, 14 (10A): 1916-1923.
CAS
PubMed Central
PubMed
Google Scholar
Paterson AH, Bowers JE, Chapman BA: Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A. 2004, 101 (26): 9903-9908.
CAS
PubMed Central
PubMed
Google Scholar
MISA - MIcroSAtellite identification tool. [http://pgrc.ipk-gatersleben.de/misa/]
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG: Primer3-new capabilities and interfaces. Nucleic Acids Res. 2012, 40 (15): e115-doi:10.1093/nar/gks596
CAS
PubMed Central
PubMed
Google Scholar
Koressaar T, Remm M: Enhancements and modifications of primer design program Primer3. Bioinformatics. 2007, 23 (10): 1289-1291.
CAS
PubMed
Google Scholar
Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F, Sudhakar D, Christou P, Snape JW, Gale MD, Harberd NP: ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature. 1999, 400 (6741): 256-261.
CAS
PubMed
Google Scholar
Plaza-Wüthrich S, Cannarozzi G, Tadele Z: Genetic and phenotypic diversity in selected genotypes of tef [Eragrostis tef (Zucc.)] Trotter. Afr J Agr Res. 2013, 8 (12): 1041-1049.
Google Scholar
Assefa K, Aliye S, Belay G, Metaferia G, Tefera H, Sorrells ME: Quncho: the first popular tef variety in Ethiopia. Int J Agr Sustain. 2011, 9 (1): 25-34.
Google Scholar
Wicker T, Matthews DE, Keller B: TREP: a database for Triticeae repetitive elements. Trends Plant Sci. 2002, 7 (12): 561-562.
CAS
Google Scholar
Salzberg SL, Yorke JA: Beware of mis-assembled genomes. Comput Appl Biosci. 2005, 21 (24): 4320-4321.
CAS
Google Scholar
Nawrocki EP, Kolbe DL, Eddy SR: Infernal 1.0: inference of RNA alignments. Bioinformatics. 2009, 25 (10): 1335-1337.
CAS
PubMed Central
PubMed
Google Scholar
Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A: Rfam: updates to the RNA families database. Nucleic Acids Res. 2009, 37 (Database): D136-D140.
CAS
PubMed Central
PubMed
Google Scholar
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A: Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 2005, 33 (Database issue): D121-D124.
CAS
PubMed Central
PubMed
Google Scholar
Chan PP, Lowe TM: GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009, 37: D93-D97.
CAS
PubMed Central
PubMed
Google Scholar
Han Y, Wessler SR: MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res. 2010, 38 (22): e199-e199.
PubMed Central
PubMed
Google Scholar
Oki N, Yano K, Okumoto Y, Tsukiyama T, Teraishi M, Tanisaka T: A genome-wide view of miniature inverted-repeat transposable elements (MITEs) in rice. Oryza sativa ssp japonica Genes Genet Syst. 2008, 83 (4): 321-329.
CAS
Google Scholar
Assefa K, Yu JK, Zeid M, Belay G, Tefera H, Sorrells ME: Breeding tef [Eragrostis tef (Zucc.) trotter]: conventional and molecular approaches. Plant Breed. 2011, 130 (1): 1-9.
CAS
Google Scholar
ABCIC: Effects Of Climate Change On Eragrostis Tef In Ethiopia: A Call For Action To Avert Food Security Crisis. ABCIC Policy Brief No1. 2011
Google Scholar
Wilson PB, Estavillo GM, Field KJ, Pornsiriwong W, Carroll AJ, Howell KA, Woo NS, Lake JA, Smith SM, Harvey Millar A, von Caemmerer S, Pogson BJ: The nucleotidase/phosphatase SAL1 is a negative regulator of drought tolerance in Arabidopsis. Plant J. 2009, 58 (2): 299-317.
CAS
PubMed
Google Scholar
Manmathan H, Shaner D, Snelling J, Tisserat N, Lapitan N: Virus-induced gene silencing of Arabidopsis thaliana gene homologues in wheat identifies genes conferring improved drought tolerance. J Exp Bot. 2013, 64 (5): 1381-1392.
CAS
PubMed Central
PubMed
Google Scholar
Akiyama T, Pillai MA: Molecular cloning, characterization and in vitro expression of a novel endo-1,3-beta-glucanase up-regulated by ABA and drought stress in rice (Oryza sativa L.). Plant Sci. 2001, 161 (6): 1089-1098.
CAS
Google Scholar
Jiang H, Li M, Liang N, Yan H, Wei Y, Xu X, Liu J, Xu Z, Chen F, Wu G: Molecular cloning and function analysis of the stay green gene in rice. Plant J. 2007, 52 (2): 197-209.
CAS
PubMed
Google Scholar
Nakashima K, Kiyosue T, YamaguchiShinozaki K, Shinozaki K: A nuclear gene, erd1 encoding a chloroplast-targeted Clp protease regulatory subunit homolog is not only induced by water stress but also developmentally up-regulated during senescence in Arabidopsis thaliana. Plant J. 1997, 12 (4): 851-861.
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic Local Alignment Search Tool. J Mol Biol. 1990, 215 (3): 403-410.
CAS
PubMed
Google Scholar
Xu JH, Messing J: Amplification of prolamin storage protein genes in different subfamilies of the Poaceae. Theor Appl Genet. 2009, 119 (8): 1397-1412.
CAS
PubMed
Google Scholar
Tatham AS, Fido RJ, Moore CM, Kasarda DD, Kuzmicky DD, Keen JN, Shewry PR: Characterisation of the major prolamins of tef (Eragrostis tef) and finger millet (Eleusine coracana). J Cereal Sci. 1996, 24 (1): 65-71.
CAS
Google Scholar
Fasteris - DNA Sequencing Service - Swiss quality. [https://www.fasteris.com/]
Functional Genomics Center Zurich. [http://www.fgcz.ch/]
Advancing through genomics. [http://www.macrogen.com/eng/]
FastQC. [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/]
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J: De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010, 20 (2): 265-272.
CAS
PubMed Central
PubMed
Google Scholar
Morgulis A, Gertz EM, Schäffer AA, Agarwala R: WindowMasker: window-based masker for sequenced genomes. Bioinformatics. 2006, 22 (2): 134-141.
CAS
PubMed
Google Scholar
RepeatMasker Open-3.0. [http://www.repeatmasker.org]
Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B: AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006, 34: W435-W439.
CAS
PubMed Central
PubMed
Google Scholar
Korf I: Gene finding in novel genomes. BMC Bioinformatics. 2004, 5: 59-doi:10.1186/1471-2105-5-59
PubMed Central
PubMed
Google Scholar
Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25 (5): 0955-0964.
CAS
Google Scholar
Schulz MH, Zerbino DR, Vingron M, Birney E: Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012, 28 (8): 1086-1092.
CAS
PubMed Central
PubMed
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W: CD-HIT: accelerated for clustering the next-generation sequencing data. Comput Appl Biosci. 2012, 28 (23): 3150-3152.
CAS
Google Scholar
Edgar RC: Search and clustering orders of magnitude faster than BLAST. Comput Appl Biosci. 2010, 26 (19): 2460-2461.
CAS
Google Scholar
Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J: TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics. 2003, 19 (5): 651-652.
CAS
PubMed
Google Scholar
Iseli C, Jongeneel CV, Bucher P: ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol. 1999, 7: 138-148.
Google Scholar
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS: Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012, 40 (D1): D1178-D1186.
CAS
PubMed Central
PubMed
Google Scholar
Schnable PS, Ware D, Fulton RS, Stein JC, Wei FS, Pasternak S, Liang CZ, Zhang JW, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, et al: The B73 maize genome: complexity, diversity, and dynamics. Science. 2009, 326 (5956): 1112-1115.
CAS
PubMed
Google Scholar
Doust AN, Kellogg EA, Devos KM, Bennetzen JL: Foxtail millet: a sequence-driven grass model system. Plant Physiol. 2009, 149 (1): 137-41.
CAS
PubMed Central
PubMed
Google Scholar
Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M, Lail K, Tice H, Schmutz J, Grimwood J, McKenzie N, Bevan MW, Huo N, Gu YQ, Lazo GR, Anderson OD, Vogel JP, You FM, Luo MC, Dvorak J, Wright J, Febrer M, Bevan MW, Idziak D, Hasterok R, Garvin DF, Lindquist E, et al: Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 2010, 463 (7282): 763-768.
CAS
Google Scholar
Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang C, Iwamoto M, Abe T, Yamada Y, Muto A, Inokuchi H, Ikemura T, Matsumoto T, Sasaki T, Itoh T: Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol. 2013, 54 (2): E6-+-
CAS
PubMed Central
PubMed
Google Scholar
Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T: Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice. 2013, 6: 4-doi:10.1186/1939-8433-6-4
PubMed
Google Scholar
Katoh K, Kuma K, Toh H, Miyata T: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005, 33 (2): 511-518.
CAS
PubMed Central
PubMed
Google Scholar
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics. 2007, 23 (21): 2947-2948.
CAS
PubMed
Google Scholar
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22 (22): 4673-4680.
CAS
PubMed Central
PubMed
Google Scholar
Guindon S, Lethiec F, Duroux P, Gascuel O: PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 2005, 33: W557-W559.
CAS
PubMed Central
PubMed
Google Scholar
FigTree. [http://tree.bio.ed.ac.uk/software/figtree/],
Li L, Stoeckert CJ, Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003, 13 (9): 2178-2189.
CAS
PubMed Central
PubMed
Google Scholar
Felsenstein J: PHYLIP - phylogeny inference package (Version 3.2). Cladistics. 1989, 5: 3-
Google Scholar
Alix B, Boubacar DA, Vladimir M: T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. Nucleic Acids Res. 2012, 40 (W1): W573-W579.
CAS
Google Scholar
Han MV, Zmasek CM: phyloXML: XML for evolutionary biology and comparative genomics. Bmc Bioinformatics. 2009, 10: 356-doi:10.1186/1471-2105-10-356
PubMed Central
PubMed
Google Scholar
Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O: Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008, 36: W465-W469.
CAS
PubMed Central
PubMed
Google Scholar
Gonnet GH, Hallett MT, Korostensky C, Bernardin L: Darwin v. 2.0: an interpreted computer language for the biosciences. Bioinformatics. 2000, 16 (2): 101-103.
CAS
PubMed
Google Scholar
Rice P, Longden I, Bleasby A: EMBOSS: the European molecular biology open software suite. Trends Genet. 2000, 16 (6): 276-277.
CAS
PubMed
Google Scholar
MISA: MIcroSAtellite identification tool. [http://pgrc.ipk-gatersleben.de/misa]
Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A: HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res. 2013, 2013: 584-589.
Google Scholar
Sigrist CJA, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I: New and continuing developments at PROSITE. Nucleic Acids Res. 2013, 41 (D1): E344-E347.
Google Scholar
Bairoch A, Bougueleret L, Altairac S, Amendolia V, Auchincloss A, Argoud-Puy G, Axelsen K, Baratin D, Blatter MC, Boeckmann B, Bolleman J, Bollondi L, Boutet E, Quintaje SB, Breuza L, Bridge A, de Castro E, Ciapina L, Coral D, Coudert E, Cusin I, Delbard G, Dornevil D, Roggli PD, Duvaud S, Estreicher A, Famiglietti L, Feuermann M, Gehant S, Farriol-Mathis N, et al: The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res. 2009, 37: D169-D174.
Google Scholar
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, et al: InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2012, 40 (D1): D306-D312.
CAS
PubMed Central
PubMed
Google Scholar
Claudel-Renard C, Chevalet C, Faraut T, Kahn D: Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res. 2003, 31 (22): 6633-6639.
CAS
PubMed Central
PubMed
Google Scholar
Delcher AL, Salzberg SL, Phillippy AM: Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinformatics. 2003, Chapter 10: Unit-Uni3.
PubMed
Google Scholar
NCBI/Blast. [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome]
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA: Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19 (9): 1639-1645.
CAS
PubMed Central
PubMed
Google Scholar