(Map markers to the barley genome - MorexV3 2021 edition)
Barleymap was designed to search the position of barley genetic markers
on the Barley Physical Map (IBSC)
,the POPSEQ map (Mascher et al.) and the
2017 Morex Genome.
The current version was updated to work with the MorexV3 genome (released in 2021).
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 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.
works on top of barleymap core API, used also in a
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.