(Map markers to the barley genome - graph 2026 edition)
Barleymap was designed to search the position of barley genetic markers
on the Barley Physical Map (IBSC[1]),
the POPSEQ map (Mascher et al.[2]) and the 2017 Morex Genome.
The current version uses by default the MorexV3 genome[5].
Since 2026 markers can also be mapped to pangenome graphs.
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.: Illumina 50K markers).
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, MorexGenome or MorexV3).
The Align to graph also requires nucleotide sequences of the markers (in FASTA format).
These will be used to retrieve their positions through alignment to the selected pangenome graph (Pan20, Med13).
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.
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.
Funding
This work was funded by DGA-Obra Social La Caixa [GA-LC-059-2011], the Spanish Ministry of Science and Innovation [AGL2010-21929,RTA2009-00006-C04-02,
PID2022-142116OB-I00], Horizon 2020 [PRIMA GENDIBAR, PCI2019-103526], Government of Aragon [A08_23R] and CSIC [FAS2022_052, INFRA24018].