Barleymap MorexV3 2021 release

Barleymap (https://floresta.eead.csic.es/barleymap), a Web tool for mapping the position of genetic markers along the physical and genetic maps of the barley genome, has been updated and now it supports the Morex V3 genome.

Previous maps, including the IBSC Barley Physical Map,the POPSEQ map and the 2017 Morex Genome, are still available linked to their mapped datasets. The current version adds to these the recently released MorexV3 genome, as taken from the INSDC archives (GCA_904849725.1) and Ensembl Plants, with slightly modified chromosome names for convenience:

>chr1H_LR890096.1
>chr2H_LR890097.1
>chr3H_LR890098.1
>chr4H_LR890099.1
>chr5H_LR890100.1
>chr6H_LR890101.1
>chr7H_LR890102.1 

The unplaced contigs have unchanged names such as:

>CAJHDD010000001.1

The following new datasets are available for MorexV3:

PGSB genes: 35,826 HC and 45,849 LC genes (e.g.: HORVU.MOREX.r3.1HG0000030).

BaRT 1.0 gene models: 45,619 genes (e.g.: BART1_0-u00002) lifted-over with litfoff

NCBI Entrez CDS: 292 sequences clustered with GET_HOMOLOGUES-EST

Illumina 50K markers: 43,078 sequences with positions provided by JHI

centromeric regions

The server now works through a secure HTTPS connection using a Let's Encrypt certificate. The web code and the standalone version are available at https://github.com/Cantalapiedra/barleymap_web and https://github.com/Cantalapiedra/barleymap respectively.

 Table. Sample output of "Align" search with dataset features decorating the region of interest. Note that by default gmap and BLASTN are used as alignment engines, supporting the alignment of genomic sequences and transcripts. Read more at https://link.springer.com/article/10.1007/s11032-015-0253-1

Please get in touch at compbio@eead.csic.es if you find anything broken,
Bruno