Excerpts from ele.ga...@tiscali.it's message of Wed Jan 12 15:19:36 +0000 2011:

> I have a problem with MAF blocks using Galaxy. 

Hi Elena, I'm copying the galaxy-user list since this is a Galaxy
related question.

> 1) the starting position of the MAF block extracted from Galaxy is
> shifted of one position downstream;

If you enter a region into the position box in the genome browser, it
will interpret it as one-based. However, when working with bed files in
Galaxy (and the genome browser) the intervals are zero-based. This is
likely the problem.

> 2) the number of species displayed is not 28 in both Maf (from Galaxy)
> and Genome Browser.

This is entirely expected. If the alignment procedure does not identify
putatively orthologous sequence in the other species, no sequence will
be shown in the MAF output for that species. There are several reasons
this could happen, including: no significant pairwise local alignment
found by lastz, or a signifigant alignment found, but eliminated 
by the chaining/netting procedure.

> 3) the alignment seems to be different (for example, species that have
> aligned sequences in the Genome Browser, are not in the MAF block
> retrieve from Galaxy).

Can you point out an example of this? In particular, are you sure you
are using the same original alignments in Galaxy and the Genome Browser?


James Taylor, Assistant Professor, Biology / Computer Science, Emory University
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