[Genome] are the "minus" strand in the "gete data" results from the galaxy browser reverse-complimented?

[Kayla Smith]

Dominik,

First, there are two ways to get sequence information from our browser. 
  The first is putting in genomic co-ordinates and clicking the "get 
DNA" button.   This will always give you genomic DNA, which is positive 
strand.  The second way is through the table browser, via the position 
information from a positional table (in this case the knownGenes table). 
  In this case, the data has the strand information attached to the 
position, and therefore, in the case of a gene on the negative strand, 
the sequence returned will be relative to that gene, or, in other words, 
the reverse complement of the genomic DNA.   It appears that you have 
proved this to yourself from your second email.

As for your second question, let me see if I understand you clearly: 
You have two bed files, one which has strand information and one which 
does not.  You would like to intersect these two bed files, and you are 
concerned that the result of the intersection may not have strand 
information in it.  Intersections in the table browser do not take 
strand information into consideration.   You would get the same output 
whether there is strand information or not.

If you are converting a BED file to FASTA format, you will get genomic 
sequence if the BED file does not have strand information in it. 
Likewise, if your BED file has strand information, you will get 
reverse-complemented-from-the-genomic sequence, for items marked 
negative.  I'm not sure exactly what you will consider proper output for 
your data analysis, but I hope I have explained the functionality of our 
tools in a way that makes sense to you.

Please don't hesitate to contact us again if you require more assistance 
with the Genome Browser.

Also, if you have any Galaxy-specific questions, they have their own 
mailing list at galaxy-user at bx.psu.edu

Kayla Smith
UCSC Genome Bioinformatics Group.


Dominik Margraf wrote:
> I have done a BLAST search on one of the FASTA sequences in the "minus
> strand" and I found that it is NOT automatically reverse-complimented
> (it actually matches the minus strand of the DNA rather than the plus
> strand).
> 
> However as mentioned in the last email, before I extract the FASTA
> sequences from the BED interval format, I intend to intersect that
> data with some other tasks (e.g. phastcon17way) which does not have
> strand info.  Then in this case will the intersection automatically
> deal with the plus vs minus strand and is it okay just feed my BED
> file for processing, then convert the resultant BED to fasta and
> reverse compliment the negative strands of the FASTA?
> 
> Thanks!
> 
> Dominik
> 
> 2006/12/5, Dominik Margraf <dominik.margraf at gmail.com>:
>> I am performing searches using the "get data" function from the Galaxy
>> browser (the known gene track) and the results are returned in BED
>> format, which I subsequently used to obtain the actual sequences in
>> FASTA format.
>>
>> However for the sequences in the "minus" strand, are these sequences
>> (in FASTA file) already reverse-complimented to the "plus strand"?  If
>> so, then would it be okay to directly use the BED file to intersect
>> with other tracks (e.g. the phastcons17way track / BED) which do not
>> have strand information?
>>
>> Thanks!
>>
>> Dominik
>>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome