Skip to Main Content

Recent Updates

21.09.2021  New page style implemented. If you happen to notice any bugs, please send an email.
12.05.2021  BLAST interface is fully functional (including blastn, tblastn, blastx, blastp).
21.04.2021  BLAST interface is working again. Currently only the blastn algorithm is functional but we will gradually improve on this feature.
13.04.2021  Morex v3 pages are now live in BARLEX. The BLAST server is available under Galaxy BLAST server. We are working to get an interface right here on this page but cannot show anything yet.
16.03.2021  Morex v3 was recently published and will be available in BARLEX soon. Currently the BLAST server is being mitigated to a new system, that is why it is not online at this moment. We are working hard to restore functionality.
24.07.2020  New Layout for BARLEX. A few less frequently used pages were moved to 'Legacy Pages' and can be reached there (see new menu on the right). Default versions for the new top menu should be Morex v2 pages.
06.07.2020  New Barley Genome Dataset and Geneset is now public (Morex v2: AGP List, Gene List, Marker). Published in Genome Biology TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools by Monat et al. (2019).
16.03.2018  Flash animations are switched to HTML5 (including BAC details view, FPC view and Cluster view).
29.08.2017  ISelect Marker tab renamed to Marker. Added Transcript Map data to Marker. Source: Stein et al. (2007): A 1000 loci transcript map of the barley genome - new anchoring points for integrative grass genomics
13.07.2017  Links to Ensembl Plants have been added for AGP List ('AGP Chromosome'), Gene List (Gene Set 2016, 'AGP Chromosome') and iSelect Marker(Morex Pseudomolecule (2016), 'AGP Chromosome'). Ensembl Plants - Hordeum vulgare
26.04.2017  New Barley Genome Sequence published. Nature article and the technical companion paper are available Scientific Data article. All Accession numbers and DOIs can be found in Supplementary Table 1.1: Nature article supplements.
19.10.2016  New Barley Genome Dataset and Geneset is now public. Downloads are available from our BLAST server.
10.06.2016  New gene set has been added, Annotation Date column added in Gene List, BAC Details View will also be changed slightly for the two different gene sets incorporated in BARLEX in the near future.
08.01.2016  You can access the BLAST server.
18.11.2015  Kmer frequency plots are now available for BAC Contigs >= 5 kb in version 4 from BAC details page.
16.11.2015  A new version of the Barley dataset is available now (version 4).
  Added new Cluster List page for Barley dataset version 4, focussed on more cluster information.
20.05.2014  A new version of the Barley dataset is available now (version 3).
04.03.2014  Expression Profiles are available at Gene details page.
24.02.2014  Added Exome Capture Target View on Morex Contig details page

BLAST

References

Mascher M, Wicker T, Jenkins J, Plott C, Lux T, Koh CS, Ens J, Gundlach H, Boston LB, Tulpová Z, Holden S, Hernández-Pinzón I, Scholz U, Mayer KFX, Spannagl M, Pozniak CJ, Sharpe AG, Simková H, Moscou MJ, Grimwood J, Schmutz J, Stein N. Long-read sequence assembly: a technical evaluation in barley. The Plant Cell (2021) koab077. dx.doi.org/10.1093/plcell/koab077
Schreiber M, Mascher M, Wright J, Padmarasu S, Himmelbach A, Heavens D, Milne L, Clavijo BJ, Stein N, Waugh R. A Genome Assembly of the Barley 'Transformation Reference' Cultivar Golden Promise. G3: Genes, Genomes, Genetics 10.6 (2020) 1823-1827. dx.doi.org/10.1534/g3.119.401010
Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M. TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome biology 20.1 (2019) 284. dx.doi.org/10.1186/s13059-019-1899-5
Bayer MM, Rapazote-Flores P, Ganal M, Hedley PE, Macaulay M, Plieske J, Ramsay L, Russell J, Shaw PD, Thomas W, Waugh R. Development and Evaluation of a Barley 50k iSelect SNP Array. Frontiers in plant science 8 (2017) 1792. dx.doi.org/10.3389/fpls.2017.01792
Beier S, Himmelbach A, Schmutzer T, Felder M, Taudien S, Mayer K F X, Plater M, Stein N, Scholz U, Mascher M. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes. Plant Biotechnol J. 14 (2016) 1511-1522. dx.doi.org/10.1111/pbi.12511
Colmsee C, Beier S, Himmelbach A, Schmutzer T, Stein N, Scholz U, Mascher M. BARLEX - the Barley Draft Genome Explorer. Molecular Plant 8 (2015) 964-966. http://dx.doi.org/10.1016/j.molp.2015.03.009
Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S, Felder M, Platzer M, Himmelbach A, Schmutzer T, Hedley P E, Muehlbauer G J, Scholz U, Korol A, Mayer K F X, Waugh R, Langridge P, Graner A, Stein N. A sequence-ready physical map of barley anchored genetically by two million SNPs. Plant Physiol. 164 (2014) 412-423. dx.doi.org/10.1104/pp.113.228213
Schmutzer T, Ma L, Poursarebani N, Bull F, Stein N, Houben A, Scholz U. Kmasker - a tool for in silico prediction of single-copy FISH probes for the large-genome species Hordeum vulgare. Cytogenet. Genome Res. 142 (2014) 66-78. dx.doi.org/10.1159/000356460
Mascher M, Muehlbauer G J, Rokhsar D S, Chapman J, Schmutz J, Barry K, Munoz-Amatriain M, Close T J, Wise R P, Schulman A H, Himmelbach A, Mayer K F X, Scholz U, Poland J A, Stein N, Waugh R. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J. 76 (2013) 718-727. dx.doi.org/10.1111/tpj.12319
Mascher M, Richmond T A, Gerhardt D J, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov E D, Hedley P E, Gonzales A M, Morrell P L, Kilian B, Blattner F R, Scholz U, Mayer K F, Flavell A J, Muehlbauer G J, Waugh R, Jeddeloh J A, Stein N. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. Plant J. 76 (2013) 494-505. dx.doi.org/10.1111/tpj.12294
Comadran J, Kilian B, Russell J, Ramsay L, Stein N, Ganal M, Shaw P, Bayer M, Thomas W, Marshall D, Hedley P, Tondelli A, Pecchioni N, Francia E, Korzun V, Walther A, Waugh R. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat. Genet. 44 (2012) 1388-1392. dx.doi.org/10.1038/ng.2447
Mayer K F X, Waugh R, Langridge P, Close T J, Wise R P, Graner A, Matsumoto T, Sato K, Schulman A, Ariyadasa R, Schulte D, Poursarebani N, Zhou R, Steuernagel B, Mascher M, Scholz U, Shi B, Madishetty K, Svensson J T, Bhat P, Moscou M, Resnik J, Muehlbauer G J, Hedley P, Liu H, Morris J, Frenkel Z, Korol A, Bergès H, Taudien S, Felder M, Groth M, Platzer M, Himmelbach A, Lonardi S, Duma D, Alpert M, Cordero F, Beccuti M, Ciardo G, Ma Y, Wanamaker S, Cattonaro F, Vendramin V, Scalabrin S, Radovic S, Wing R, Morgante M, Nussbaumer T, Gundlach H, Martis M, Poland J, Pfeifer M, Moisy C, Tanskanen J, Zuccolo A, Spannagl M, Russell J, Druka A, Marshall D, Bayer M, Swarbreck D, Sampath D, Ayling S, Febrer M, Caccamo M, Tanaka T, Wannamaker S, Schmutzer T, Brown J W S, Fincher G B, Stein N. A physical, genetic and functional sequence assembly of the barley genome. Nature 491 (2012) 711-716. dx.doi.org/10.1038/nature11543
Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K, Kikuta A, Kamiya K, Yamamoto M, Ikawa H, Fujii N, Hori K, Itoh T, Sato K. Comprehensive Sequence Analysis of 24,783 Barley Full-Length cDNAs Derived from 12 Clone Libraries. Plant physiology 156.1 (2011) 20-28. dx.doi.org/10.1104/pp.110.171579
Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney RK, Perovic D, Grosse I, Graner A. A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theoretical and Applied Genetics 114.5 (2007) 823-839. dx.doi.org/10.1007/s00122-006-0480-2

How to cite

Colmsee C, Beier S, Himmelbach A, Schmutzer T, Stein N, Scholz U, Mascher M. BARLEX - the Barley Draft Genome Explorer. Molecular Plant 8 (2015) 964-966. http://dx.doi.org/10.1016/j.molp.2015.03.009
Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Simkova H, Stankova H, Vrana J, Chan S, Munoz-Amatriain M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Dolezel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature 544 (7651):427-433. http://dx.doi.org/10.1038/nature22043
Beier S, Himmelbach A, Colmsee C, Zhang XQ, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Simkova H, Stankova H, Vrana J, Chan S, Munoz-Amatriain M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Houben A, Dolezel J, Ayling S, Lonardi S, Langridge P, Muehlbauer GJ, Kersey P, Clark MD, Caccamo M, Schulman AH, Platzer M, Close TJ, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M (2017) Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Sci Data 4:170044. http://dx.doi.org/10.1038/sdata.2017.44