Howdy, Tom,
I'm the author of lastz. I hadn't been on that mailing list, but a
colleague forwarded your message to me. I've now joined the list.
(a) I cannot find a way to compare multiple fasta with multiple fasta.
I'm not entirely sure what you are trying to do with multiple fasta.
One guess is you want to align a gourp of aligned sequences with
another group of aligned sequences.
Lastz is a pairwise aligner, single sequence to single sequence. It
does have some support for comparing profile sequences (called
'quantum DNA' in the documentation). This was intended to be useful
for aligning alignments to alignments, but it has limited practical
use as implemented. Our lab also produced multiz and tba, two
aligners that build multiple alignments from pairwise alignments.
Those should be available here:
www.bx.psu.edu/miller_lab
Another guess is that you have a bunch of sequences in one fasta file,
and you want to align them all vs each other. The simplest way to do
this is to just list that file twice on the command line, as both the
target and as the query, e.g. "lastz file.mfa[multiple] file.mfa".
For compatibility with blastz, though, lastz does not accept a file
with more than one sequence as the target (first file) unless you
attach "[multiple]" to the end of the file name. The other issue is,
if all those sequences combined are more than 2 billion bases, you
will need to build a version of lastz that supports that. I can
describe how to do that if that's what you need.
(b) Is there any ways to [compare one chromosome and other
chromosomes] in a quick fashion?
To get quick answers about alignability, I usually use lastz's
ungapped alignments and restrict seeding. This can usually give you a
good picture of what aligns to what. This is described here:
www.bx.psu.edu/~rsharris/lastz/newer/README.lastz-1.03.02.html#ex_chrom
Let me know if that helps, or not,
Bob H
> ---------- Forwarded message ----------
> Date: Tue, 31 Jul 2012 17:49:21 +0800
> From: wangdp <[email protected]>
> Subject: [Genome] Lastz tools
> To: genome <[email protected]>
> Message-ID: <[email protected]>
> Content-Type: text/plain; charset="gb2312"
>
> Dear UCSC team:
>
> I am now using the lastz tool to compare one species with itself.
>
> But I cannot find a way to compare multiple fasta with multiple
> fasta. Furthermore, it need much more time to compare one chromosome
> and other chromosomes.
>
> Could you please help me about the two issues?
>
> Is there any ways to do it in a quick fashion?
>
> Thanks a lot and best wishes,
>
> Sincerely,
>
> Tom
>
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