Question: Genbank file format is wrong?
0
gravatar for eddie.im
4.8 years ago by
eddie.im130
Brazil
eddie.im130 wrote:

Hello,

I'm having a hard time to understand the logic behind the Genkbank file format. In special about the "complement" feature, which doens't seems to make sense to me, can someone help me out?

When i'm reading through a full genbank genome file, there is some annotations like: complement(1..200).

So lets say that my genome has 1000bp, What i'm expecting is that i'm pulling the sequence from range 1 to 200 of the reverse complement of the sequence in the end of the file (which i assume that is the "plus" strand" like on the exemple bellow:

       real
 1  ----------------------------------------------------- 1000

1000----------------------------------------------------- 1
      possible**                              expected

**The other possible logic is that the ranges points to reverse complement (which would be 800..1000 of the reverse strand in my logic) , but it's not the case either.

 

But its seems that no matter if it's complement or not the sequence is always pulled from the plus strand directly, it's not even pulled then reverse complemented, it's just pulled directly from the plus strand even tough it's pointing to the reverse strand.

 

I must be missing something... can someone make this clear for me?
Thanks in advance

file genbank reverse • 1.8k views
ADD COMMENTlink modified 4.7 years ago by Biostar ♦♦ 20 • written 4.8 years ago by eddie.im130
2
gravatar for Zhaorong
4.8 years ago by
Zhaorong1.2k
State College, PA
Zhaorong1.2k wrote:

I don't quite get your question. But reading this may help: http://www.insdc.org/files/feature_table.html#3.4.3

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Zhaorong1.2k

Hi Zhaorong, thanks a lot! It helped me!

ADD REPLYlink written 4.8 years ago by eddie.im130
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