Latest changes
31-05-2024:
. MorexV3 HC genes in maps now link out to multiple protein alignments of barley pangenes, read more at the
blog.
08-02-2024:
. Check out barley pangenes and their conservation at
https://eead-csic-compbio.github.io/barley_pangenes
22-08-2023:
. Results can now be correctly exported as CSV files after fixing bug.
19-06-2023:
. Mapped DartSeq markers on MorexV3 by user request.
15-03-2023:
. Moved to new server and updated URL (
https://barleymap.eead.csic.es).
14-06-2022:
. Added lifted-over IBSC 2012 & 2016 gene models to MorexV3 map.
04-11-2021:
· Added MorexV3 map + centromeres, PGSB and BaRT1.0 gene models and NCBI Entrez CDS sequeces (see release
notes).
17-08-2018:
· Added POPSEQ map updated with 2017 data
[3] (POPSEQ_2017).
6-03-2018:
· Added a dataset of NCBI genes to the Morex Genome map. This dataset includes genes like HvCO1, Int-c, Btr1, Vrs1, PhyB, HvCEN, etc... to a total of 894 entries.
19-12-2017:
· Support for the
Illumina50K[4] markers, which can now be searched in the
IBSC
[1], POPSEQ
[2] and Morex Genome
[3] released in 2017,
through the
Find markers option.
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 was updated to work with the
MorexV3 genome (released in 2021)
[5].
All the public data used by Barleymap can be found at
PGSB
,
IPK
,
e!DAL
,
Barley RTD
the
NCBI
and https://eead-csic-compbio.github.io/barley_pangenes
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.
In addition to locate a list of markers or sequences,
information of genes and pangenes, 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
Computational and structural biology group
(
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: 718-27. doi:10.1111/tpj.12319
[3]Mascher et al. 2017
A chromosome conformation capture ordered sequence of the barley genome
Nature. 544:427-433. doi:10.1038/nature22043
[4]Bayer et al. 2017
Development and Evaluation of a Barley 50k iSelect SNP Array
Frontiers in Plant Science. 8:1792. doi:10.3389/fpls.2017.01792
[5]Mascher et al. 2021
Long-read sequence assembly: a technical evaluation in barley
The Plant Cell 33(6):1888–1906 doi:10.1093/plcell/koab077
[6]Rapazote-Flores et al. 2019
BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq
BMC Genomics 20:968 doi:10.1186/s12864-019-6243-7
[7]Contreras-Moreira et al. 2023
GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation
Genome Biol 24, 223 doi: 10.1186/s13059-023-03071-z
