Question: Negative Strand Coordinates in Fasta Files?
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gravatar for ad
3.7 years ago by
ad30
United States
ad30 wrote:

Hi, I've obtained the arabidopsis gene list in fasta format from ensembl and I was wondering whether coordinates from genes on the negative strand such as I think, this one..

>ATMG01410.1 cdna:known chromosome:TAIR10:Mt:366086:366700:-1 gene:ATMG01410 transcript:ATMG01410.1 description:"Uncharacterized mitochondrial protein AtMg01410"

 have to be converted to positive strand coordinates or are they all the same positive strand coordinates? I assume the coordinates are 366086:366700. Do you have to do anything with them or can they simply be plugged right into a genome browser?

Thanks

dna sequencing assembly • 1.7k views
ADD COMMENTlink modified 3.7 years ago by RamRS21k • written 3.7 years ago by ad30
0
gravatar for Brice Sarver
3.7 years ago by
Brice Sarver2.6k
United States
Brice Sarver2.6k wrote:

Usually positions are relative to the positive strand (or at least they are in most mouse databases - I had the same question as you a while ago). You can validate this by extracting the sequence based on those coordinates and seeing whether or not you need to reverse complement them to get the correct sequence.

ADD COMMENTlink written 3.7 years ago by Brice Sarver2.6k
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gravatar for RamRS
3.7 years ago by
RamRS21k
Houston, TX
RamRS21k wrote:

Co-ordinates are usually only given to one strand. You can use them to view the region, and browsers generally have an option to reverse the sequence being displayed - that should get you the co-ordinates decreasing as opposed to increasing when you move left to right. You'll still need to complement the sequence in the region once you extract it though (if you're going from co-ordinates to sequence).

While for most operations you'll need the reverse complement of the reference sequence, if you're trying to represent a variant you'd have to go with the actual reference strand base.

ADD COMMENTlink written 3.7 years ago by RamRS21k
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