[Genome] can you provide some pairwise alignments for me

[Brooke Rhead]

Hello Jian-Hua,

We do not have plans to do more work on the assemblies you mention at 
this time; we are invested in other efforts.

However, we may already have some of the pairwise alignments in which 
you are interested.  We are planning to release full assemblies on five 
nematodes very soon.  They will be:

Caenorhabditis elegans (Jan 2007) - ce4
Caenorhabditis brenneri, aka: Caenorhabditis n. sp. 4. PB2801 (Jan 2007) 
- caePb1
Caenorhabditis briggsae (Jan 2007) - cb3
Caenorhabditis remanei (Mar 2006) - caeRem2
Pristionchus pacificus (Feb 2007) - priPac1

We have generated pairwise alignments between each of these five 
assemblies.  The assemblies are currently on our test server, at 
http://genome-test.cse.ucsc.edu/.  Be aware that some of the data on our 
test server has not gone through our usual quality assurance process.

It looks like you may already be using the test server for the C. 
savignyi and Lancelet genomes.  The only pairwise alignment we have for 
C. savignyi is to C. intestinalis (cioSav1/ci1).  The only pairwise 
alignment we have for Lancelet is to human (braFlo1/hg18).  Let us know 
if you would like to download either of these.

I'm sorry we can't be of more assistance.  You might check with WormBase 
(http://wormbase.org/) to see if they are planning on generating any of 
these pairwise alignments.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Yang Jianhua wrote:
> Dear UCSC Bioinformatics Group,
> 
> I try to find snoRNA genes in Deuterostome and Nematode clade(C.savignyi, 
> Lancelet,C.elegans,etc.) using our progam snoSeeker(publish in NAR). 
> However, I can't download pairwise alignment sequences(Axt format) for these 
> genomes. Can you provide pairwise alignment sequences for me? 
> 
> Thank you very much!
> 
> Best  regards, 
> Jian-Hua
> /**************************************************
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> ***************************************************/
> 
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