[Genome] obtaining multiz17way alignments batch wise

[Rachel Harte]

Robert.
You can obtain the MAF format file through the Table Browser for all the
species in the multiz17way alignment starting with a list of human 
coordinates.  First you will need to make a custom track for the 
human coordinates and then you will need to intersect the multiz17way
track with the custom track.

To create a custom track, click on the "add custom tracks" button on 
the Gateway page or below the Browser image which will take you to here:
http://genome.ucsc.edu/cgi-bin/hgCustom?

Here there are instructions for making a custom track. The easiest way to 
do it would be to make a BED format list of the human coordinates. BED 
format is described here:
http://genome.ucsc.edu/FAQ/FAQformat#format1

Note that all start coordinates are 0-based for BED format so base 
position 1 is 0.

Once you have created the track, you will be taken to a custom tracks 
management page. Click on the button "access in table browser".

Now you are ready to do the Table Browser intersection:

1) On the Table Browser and select human and the assembly of interest.
2) Select Comparative Genomics as the group, Conservation as the track and 
multiz17way as the table.
3) Make sure that you have genome selected as the region.
4) Click on the create button for intersection and select Custom Tracks as 
the group and select the custom track that you created.
Also select "Base-pair-wise intersection (AND) of Conservation and User 
Track". This will make sure that you get only the regions of the 
alignments that are in the regions defined in your custom track. The 
Press submit.
5) Select MAF as the output format and press "get output".

The result should be those regions of the multiz17way alignment that 
are in the regions specified by the set of human coordinates in your 
custom track.

I hope that this helps you. Please let us know if you have further 
questions.

Rachel

  On Tue, 10 Oct 2006, Robert 
Querfurth wrote:

> Hello,
>
> is it possible via the Table Browser to obtain, starting from a list of
> human coordinates, the orthologous sequences in fasta or MAF format for
> all available species?
> and if so, how.
>
> thank you very much,
> Robert Querfurth
>
> ---
> Department for Vertebrate Genomics
> Max Planck Institute for Molecular Genetics
> Ihnestrasse 73
> 14195 Berlin
> Germany
>
> +49 30 8413 1225
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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>

-- 
Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu