Barleymap graph now produces FASTA

Following a recent post where we released Barleymap graph, today I show here a new feature that we realized was needed, namely the sequences of the regions matched in the graph. 

Input: we will illustrate this with the genomic sequence AY750993.1, which corresponds to the MADS-box transcription factor BM5A (VRN-H1) gene from barley cultivar Strider, which contains 7 introns that harbour transposons. Overal, the Strider sequence is 17,220bp long.

1. Paste the AY750993.1 sequence in FASTA format in https://barleymap.eead.csic.es/barleymap/graph

2. Lower the min. identity cutoff to 95%. Only by doing this we recover a match from HOR_21599.

3. Press  ; after a few seconds you will get a table results. The important part here is the 'other alignments' column:

chr5H@MorexV3:528147864-528156753(-)
chr5H@Hockett:529179413-529188302(-)
chr5H@Igri:536576211-536592410(-)
chr5H@Du_Li_Huang:531951537-531956948(-)
chr5H@Planet:536046041-536053321(-)
chr5H@HOR_9043:529479374-529486654(-)
chr5H@Barke:538056728-538062023(-)
chr5H@HOR_13821:532398401-532414507(-)
chr5H@HOR_21599:525404342-525419909(-)
chr5H@HOR_3365:526478073-526494180(-)
chr5H@HOR_8148:527939009-527947898(-)
chr5H@HOR_13942:533891783-533900845(-)
chr5H@GoldenPromise:528765071-528773960(-)
chr5H@B1K-04-12:541668530-541688540(-)
chr5H@HOR_10350:523238019-523245299(-)
chr5H@HOR_7552:531092836-531098247(-)
chr5H@OUN333:528472375-528482213(-)
chr5H@Chiba:530164325-530180432(-)
chr5H@Akashinriki:530911309-530916720(-)
chr5H@HOR_3081:531132876-531148982(-)
FASTA

4. Right-click on the FASTA link and save the FASTA file to your local file system.

5. You can now inspect the sequences that correspond to the ranges in 'other alignments' column:

perl -lne 'print substr($_,0,40)' Pan20_mmap_pro.bmap-AY750993.1-95.0-98.0p4v87ssv.fna

>chr5H@MorexV3:528147864-528156753(-)
TAACCCAGTCGCCAACATCAAAAGAAAGGGCCTGATGTTT
>chr5H@Hockett:529179413-529188302(-)
TAACCCAGTCGCCAACATCAAAAGAAAGGGCCTGATGTTT
>chr5H@Igri:536576211-536592410(-)
TATTGATGGGTGGAGGACTGGTCGGCGCACACGCGCGCAC

...

6. You can run a multiple sequence alignment and get something similar to this: 

Take care, Bruno