[Genome] 28-way protein sequence alignment

[Ann Zweig]

Hello Li,

	This is something that we are intending to create in the near future.  Protein 
alignment tracks will be available for many assemblies that currently have 
multiple alignments in DNA-space.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Li, Leping (NIH/NIEHS) [E] wrote:
> Hello again,
> 
> The steps outlined gave me the multiz alignment of genomic sequences
> rather than protein sequences I need. What I would like to obtain is the
> multiz alignment of protein sequences for a human protein query
> sequence.
> 
> Thanks again.
> 
> Leping Li
> NIEHS/NIH
> 
> -----Original Message-----
> From: Kayla Smith [mailto:kayla at soe.ucsc.edu]
> Sent: Thu 12/6/2007 7:20 PM
> To: Li, Leping (NIH/NIEHS) [E]
> Cc: genome at soe.ucsc.edu
> Subject: Re: [Genome] 28-way protein sequence alignment
>  
> 
> Hello Leping,
> 
> First you need to find genomic coordinates that correspond to your 
> sequence.   You can use BLAT to help you find where your protein 
> sequence is located.
> 
> Here is a link to BLAT:
> 
> Next, use the Table Browser ("Tables", on the blue bar on the top of the
> 
> main page) to get the data you're interested in.  Set the following
> options:
> 
> clade: Vertebrate
> genome: Human
> assembly: Mar2006
> group: Comparative Genomics
> track: Conservation
> table: multiz28way
> position (paste in your genomic coordinates here!)
> output format:  MAF- multiple alignment format.
> 
> Press "get output"
> 
> I hope this is helpful to you.  Please don't hesitate to contact us 
> again if you require further assistance.
> 
> Kayla Smith
> UCSC Genome Bioinformatics Group
> 
> 
> Li, Leping (NIH/NIEHS) [E] wrote:
>> Hi,
>>
>>  
>>
>> I have a short human protein sequence. I would like to obtain the
> multiz
>> alignment of the protein sequences rather than the DNA sequences. I'd
>> appreciate your help. Thanks.
>>
>>  
>>
>> Leping Li
>>
>> NIEHS/NIH
>>
>>  
>>
>>  
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
> 
> 
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome