[Genome] Genomic Alignment

[Kayla Smith]

Hello Stefanie,

Information on how genes are aligned to the genome can often be found by 
clicking into a track's details page.  For example, here is the details 
page for the UCSC Genes track:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?c=chrX&g=knownGene

And here is some information on BLAT:

http://genome.ucsc.edu/FAQ/FAQblat

You might also find it insightful to turn on the chain and net tracks in 
the browser for the species for which you are looking for homology.

This should help you get started.   Please don't hesitate to contact us 
again if you require further assistance.


Kayla Smith
UCSC Genome Browser

Stefanie Figura wrote:
> Dear all!
> 
> I´ve a question about how the genomic alignments are done in the UCSC browser when a gene is located on different strands in the species which should be included in the alignment. I´m interested in a gene in the rat genome (itga11) which is  located on the plus strand and in the human genome on the minus strand. Is the genomic sequence inverted (to get the same direction)?
> 
> For instance:
> 
> ATGGC on minus strand in human is inverted to
> CGGTA to align it to the homologous sequence in the rat genome?
> 
> I hope somebody can help me with this trivial question.
> Thanks in advance!
> 
> Kind regards,
> Stefanie
>