Barleymap

(Map markers to the barley genome - Morex Genome 2017 edition)

Barleymap was designed to search the position of barley genetic markers on the Barley Physical Map (IBSC[1]) and the POPSEQ map (Mascher et al.[2]). The current version was updated to work with the Morex Genome (released in 2017)[3].

All the public data used by Barleymap can be found at MIPS FTP server , IPK FTP server, and FTP server for Morex Genome 2017 data.

The Find markers option allows to find the position of markers by using their identifiers as input.
Note that those markers must be part of one of the precalculated datasets available (e.g.: iSelect Infinium 9K).

To use the Align sequences option you must provide nucleotide sequences of the markers (in FASTA format).
These will be used to retrieve their positions through sequence alignment to the selected map (IBSC2012, POPSEQ or MorexGenome).

The Locate by position option allows to examine the map context of specific positions, which must be provided as tuples with chromosome (or contig) and position (local position, within the chromosome or contig, in base pairs). For example, an user could provide as input "chr1H 10000" to find out which genes are in that specific region of chromosome 1H.

In addition to locate a list of markers or sequences, information of genes, genetic markers, and anchored features, that enrich the context around or between the queries will be shown.

Barleymap web works on top of barleymap core API, used also in a standalone application that allows loading custom databases, maps and datasets, among other features.
Such application can be used with data from any organism for which sequences anchored to a genetic/physical background are available.

Further information about how this tool works and help on using it can be found here.
Or you may wish to contact the Laboratory of Computational Biology (EEAD - CSIC):
Carlos P Cantalapiedra
Bruno Contreras-Moreira

Citation: Cantalapiedra CP, Boudiar R, Casas AM, Igartua E, Contreras-Moreira B. BARLEYMAP: physical and genetic mapping of nucleotide sequences and annotation of surrounding loci in barley. Mol Breeding (2015) 35:13 DOI 10.1007/s11032-015-0253-1



[1]IBSC. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature. 491:711-16. doi:10.1038/nature11543
[2]Mascher et al. 2013. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). The Plant Journal, 76: 718–727. doi: 10.1111/tpj.12319
[3]In press



Last changes

This is an early deployment of Barleymap Morex Genome 2017 edition. Therefore, the main updates from the previous POPSEQ edition to this Morex Genome 2017 edition are explained next. Note that most of this information will be included, and more detailed, in the Help section in the near future. This is also true for the standalone application, which is in general updated but the help files are not.

2017-03-30:
· New Locate by position action available.

· Support for the Morex Genome released in 2017.

· New datasets have been added, to be searched with Barleymap Find, including: BOPA1, BOPA2, iSelect Infinium 9K, Darts, DartSeq, GBS SNPs from OWB, Haruna Nijo flcDNAs, HarvEST 36 tags, IBSC2012 genes ("MLOCs"), IBSC2016 genes ("HORVUs"), and IBSC2012 BacEndSequences (BES), sequenced BACs, and IBSC2012 WGS contigs from Barke, Bowman and Morex. Illumina 50K will be available whenever its metadata is made public. Note that not all this datasets can be searched in the three maps. For example, HORVUs are limited to MorexGenome (2017), whereas Barke WGS contigs can only be found in IBSC2012 and MorexGenome, but no in POPSEQ; Morex WGS contigs can be found in all three maps. Finally, some of these datasets can be queried with different synonyms. For example, BOPA1 markers (e.g.: BOPA1_10114-1946, 10114-1946), or iSelect Infinium 9K markers (e.g.: i_SCRI_RS_100054, SCRI_RS_100054; or i_11_10006, 11_10006, 1016-376, BOPA1_1016-376).

· IBSC2012 BES, sequenced BACs and WGS contigs are not genes nor markers, but a different kind of feature which we called anchored features. Besides searching them by identifier, anchored features close to map positions obtained can be included in the output map through the enrichment options. This allows including, for example, the position of Morex WGS contigs in the output map. However, note that the enrichment with anchored features is slow, so we encourage you to use enrichment of anchored features only when really needed.

· A new option "show only main features", has been added in the "enrichment" options section. When checked, the output map will include, as additional features, only the main ones (for example, the HORVUs in the MorexGenome, but no the MLOCs or the flcDNAs). When unchecked, the enrichment process will be slower, but all the available features will be included in the output map (in the previous example, MLOCs, flcDNAs, and other genes will be included along with HORVUs).

· The results tables have been remodelled. Now, the enriched features are shown in line with the queries, but in a different background color. In the downloadable CSV files, both row types are differentiated with the first field of the table.

· Also in the results page, an icon has been included to zoom in the markers of interest in the graphical chromosomes.

· There are other minor changes, and more of them in the standalone application and the core API.