[Genome] Chimp assembly 2 pairwise alignments

[Archana Thakkapallayil]

Hello Dan,

Here is the response from one of our engineers:

I think that the easiest way to do this is using Galaxy 2. This method 
will involve using the pairwise alignments extracted from the multiz 
multiple alignment (from the Conservation track). This is a best in 
genome alignment with the best aligning region for chimp aligned to each 
region of the human genome. This means that there is less information 
than in the chain track which contains all alignments (passing certain 
criteria) of the chimp genome to each region of the human genome. If 
this is ok, then you can use Galaxy by going to:
http://test.g2.bx.psu.edu/

You will need to use the test version of Galaxy because this has the 
option of using our genome-test server. There are only panTro1 
alignments in the 17-way alignment on hg18, but there are panTro2 
alignments in the 28-way on hg18. Be aware that this our test server and 
that some of the data here (including the 28-way alignment) has not gone 
through our rigorous quality assurance checks.

Here are the instructions to follow:

1) Go to http://test.g2.bx.psu.edu/
2) Click on "Get Data" in the pane at the left side.
3) Click on "UCSC Test table browser" link in the expanded list.
4) In the middle an interface will appear that looks like the Table 
Browser. You can then select the Human Mar 2006 (hg18) assembly. Select 
Comparative Genomics as the group, 28-way Cons as the track and 
"multiz28wayAnno" as the table. Make sure that genome is selected as the 
region. Then select MAF as the output type.
5) Check the box that says "Send output to Galaxy". Press "get output" 
button and the "Send query to Galaxy" button. (Up to this point can also 
be done in the Table Browser on genome-test). Getting the MAF output 
seems to be rather slow.
6) Then from the "Get Data" menu, select "Upload File" and you can paste 
in or upload a file of the regions for which you want alignments 
(position or BED format is fine).
7) Then click on the "Fetch Sequences and Alignments" in the left pane.
 From the expanded list, select "Extract MAF blocks". First select the 
genomic intervals (query 2) and then press "Next Step" and select the 
MAF format output (query 1). The result is the multiple alignments for 
the regions defined by the user.
8) To limit this to only the pairwise alignment between human and chimp, 
select the "Maf Limit to Species" from the left pane and choose hg18 and 
panTro2.

If you have questions about using Galaxy, you can contact their help desk:
galaxy-user at bx.psu.edu

If you would rather use the human/chimp chain or net alignments to get 
alignments for specific regions of the human genome, then we can walk 
you through using several of the programs that we have available for 
command line use in order to extract human/chimp pairwise alignments 
from this data.

I hope this information is helpful to you. Let us know if you have 
further questions.

Regards,

Archana
UCSC genome Bioinformatics Group



Daniel Gaffney wrote:
> Hi there,
> I have ~ 1500 small regions in the human genome, for which I would like 
> to get the human-chimp
> pairwise alignment for the latest chimp assembly. However, I'm having a 
> little trouble in figuring out the best
> way to do this - can this be done locally? Or is there a batch 
> submission tool that I can retrieve all alignments
> from UCSC directly - I've tried the table browser, but I can't seem to 
> get the specific region I want (i.e. if i select the chimp chain
> track, and retrieve sequence, I get the the alignment of that entire 
> region, not just the region corresponding to the coordinates I've
> entered). Any ideas?
> Cheers
> Dan
>
>