[Genome] gene alignment

[Brooke Rhead]

Hello Krista,

There are two ways you could go about finding fly-human alignment 
information.

First, there are human protein and mRNA alignments to fly in a couple of 
tracks on the dm2 Genome Browser: the "Human Proteins" track and the 
"Other mRNAs" track.  If you type 'LanA' in the search position box on 
the dm2 browser and turn on these two tracks, you will see two 'Lama5' 
proteins aligned in the "Human Proteins" track and one human mRNA 
aligned in the "Other mRNAs" track (BC085017).  To make it easier to 
find the human mRNA of interest, click on the blue "Other mRNAs" link 
(right above the drop-down menu that controls the track visibility) to 
get to the track controls page.  Enter 'lama5' in the gene field and hit 
submit.  This will filter the mRNAs for your gene of interest and 
display it in red at the top of the track.  Click on the individual 
items in each track to view the alignment details and to read about how 
the alignments were done.

The other option for finding alignments is to use NCBI's online BLAST 
server to do the alignments yourself.  Follow the Protein-protein BLAST 
(blastp) link on this page:

http://www.ncbi.nlm.nih.gov/BLAST/

Or, if you would like to download NCBI's BLAST suite and run the 
programs yourself, there is some helpful information at both of these sites:

http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html
http://en.wikipedia.org/wiki/BLAST

I hope this information is helpful to you.  If you have any more 
questions or need clarification on the Genome Browser instructions 
above, please do not hesitate to write back to this list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Krista R Casazza wrote:
> Hi 
> I am a postdoc at UAB and we are looking at a gene in drosophila LanA on
> chromosome 3L that is involved in fat storage.  An ortholog Lama5 is on
> chromosome 20 in humans.  I am trying to determine if there is alignment
> or conservation between the 2 genes.  I got the fly sequence from
> ensembl and the human sequence from Entrez SNP and ran it through BLAT
> but got no hits.  It was suggested that BLAT may not be sensitive enough
> to pick up human/fly orthologs, as BLAT, for the most part, was written
> to map mRNAs and traces back to
> the genome, or a closely related genome, very quickly. It was also
> suggested that I probably want to do the alignments with a program like
> blastp.  I have attached the text format of the genes.  Is it possible
> for you to help me with this alignment.  As you can probably ascertain,
> my PhD is not in genetics and this research is very new to me.  I would
> appreciate any assistance that you may have to offer.
> Thanks 
> Krista
>  
> Krista Casazza, PhD, RD
> Postdoctoral Fellow
> University of Alabama at Birmingham
> WEBB 415
> 1675 University Blvd.
> Birmingham, AL 35294
> (205) 975-6226
> 
> 
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