Why is the UCSC genome browser sequence a complement of the BDGP5 sequence?
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9.9 years ago
mjs • 0

Why is the sequence shown in the UCSC genome browser a complement of the BDGP5 sequence (fasta downloads from FlyBase and ensembl)?

The fasta download from FlyBase for a particular region:

>2L:8438269..8438280 species=Dmel; strand='+'; loc=2L:8438269..8438280;
CTTTCCAGCACT

The UCSC genome browser displays a sequence as follows (screen shot below):

GAAAGGTCGTGA

which is a complement of the FlyBase sequence.

The strand information is important for the analysis that I am doing so I would like to understand the discrepancy and ensure that the FlyBase sequence is indeed on the + strand. FYI, the HUMAN fasta download from biomart from ensembl and the UCSC sequence are identical.

Any help would be appreciated!

drosophila fruit fly ucsc complement sequence • 2.3k views
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you have linked an image that seems to be in the trash

http://genome.ucsc.edu/trash/hgt/hgt_genome_7d67_aa0870.png
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