Question: Why is the UCSC genome browser sequence a complement of the BDGP5 sequence?
0
gravatar for mjs
5.8 years ago by
mjs0
United States
mjs0 wrote:

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!

ADD COMMENTlink written 5.8 years ago by mjs0

you have linked an image that seems to be in the trash

http://genome.ucsc.edu/trash/hgt/hgt_genome_7d67_aa0870.png
ADD REPLYlink modified 8 weeks ago by RamRS25k • written 5.8 years ago by Istvan Albert ♦♦ 82k
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