This track shows the alignments of selected full genome sequences in Genbank to the reference genome.
Alignable regions are shown with thick lines. Small single-bp differences are highlighted with red tickmarks on the thick lines. Alignable regions can be separated by non-alignable sequences with thinner lines. Deletions are shown with single lines. Deletions that include at least one short insertion are shown with double lines. Rearrangements are not shown directly, but duplications will lead to two rows of thick lines, with the exact origin of the sequence shown on mouse over or by clicking the sequence.
Sequences were aligned with BLAT and filtered with our command line tool pslReps at default settings.
The raw data can be explored interactively with the Table Browser or combined with other datasets in the Data Integrator tool. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server.
Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed. Instructions for downloading this command can be found on our utilities page. The tool can also be used to obtain features within a given range without downloading the file, for example:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/mpxvRivers/genbankAli/seqs.bb -chrom=NC_063383.1 -start=0 -end=100000 stdout
Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.
Monzon S et al, Genomic accordions may hold the key to Monkeypox Clade IIb's increased transmissibility Biorxiv Oct 01, 2022
Gigante CM et al, Genomic deletions and rearrangements in monkeypox virus from the 2022 outbreak, USA Biorxiv, Sep 17 , 2022