The RefSeq mRNAs gene track for the 08 Dec 2016 Aspergillus brasiliensis CBS 101740/GCF_001889945.1_Aspbr1 genome assembly displays translated blat alignments of vertebrate and invertebrate mRNA in GenBank.
Download GCF_001889945.1_Aspbr1.xenoRefGene.gtf.gz GTF file.
Total genome size: 35,804,080
Gene count: 1,481
Bases in genes: 3,276,815
Percent genome coverage: % 9.152
The mRNAs were aligned against the Aspergillus brasiliensis CBS 101740/GCF_001889945.1_Aspbr1 genome using translated blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only those alignments having a base identity level within 1% of the best and at least 25% base identity with the genomic sequence were kept.
Specifically, the translated blat command is:
blat -noHead -q=rnax -t=dnax -mask=lower target.fa query.fa target.query.psl where target.fa is one of the chromosome sequence of the genome assembly, and the query.fa is the mRNAs from RefSeqThe resulting PSL outputs are filtered:
pslCDnaFilter -minId=0.35 -minCover=0.25 -globalNearBest=0.0100 -minQSize=20
-ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap
all.results.psl GCF_001889945.1_Aspbr1.xenoRefGene.psl
The filtered GCF_001889945.1_Aspbr1.xenoRefGene.psl is converted to
genePred data to display for this track.
The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779
Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518