# downloaded cdcSeqs1.fa and hgq.fa manually from Genbank. Should use NCBI command line tool for that
# sequences were made by pasting accessions received from authors into a text file.
cd /hive/data/genomes/mpxvRivers/bed/genbankAli/
cat cdcSeqs1.fa hgq.fa > seqs.fa
blat ../../mpxvRivers.unmasked.2bit seqs.fa seqs.psl -noHead
pslReps seqs.psl seqs.filt.psl out.psr
pslToBigPsl -fa=seqs.fa seqs.psl stdout | sort -k1,1 -k2,2n > seqs.bed
bedToBigBed -as=${HOME}/kent/src/hg/lib/bigPsl.as -type=bed12+13 -tab seqs.bed ../../chrom.sizes seqs.bb