[Genome] (no subject)

[Archana Thakkapallayil]

Hello Shauna,

We do have a tool for aligning sequences called 'BLAT' on our browser:
http://www.genome.ucsc.edu/cgi-bin/hgBlat

However, you could only BLAT your sequences against the database that 
you selected. You are also limited to the approximately 70 genomic 
assemblies that we have on our website. You may have sequence from 
species that we do not host on our site. You can scroll through the list 
of species that we have on our site here:
http://genome.ucsc.edu/goldenPath/releaseLog.html

You can read more about BLAT here:
http://www.genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign

You might consider using the tool 'BLAST' provided by NCBI:  
http://www.ncbi.nlm.nih.gov/BLAST/
BLAST lets you input your data without choosing a genome. In either case 
you will have to convert your .abi format to FASTA file format. Here is 
link that might be useful for converting .abi to FASTA:
http://www.mybio.net/biowiki/Sequence_format_conversion

Also, I am not sure if you are trying to generate a multiple alignment 
with your sequences. If so, we don't provide any tools for multiple 
alignments. Here are some links to standard genome multiple alignments 
programs such as:

ClustalW - http://www.ebi.ac.uk/clustalw/
The program can also be downloaded via link from this site.
MAFFT - http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/
T-Coffee - http://www.ebi.ac.uk/t-coffee/
and others: http://pbil.univ-lyon1.fr/alignment.html

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Regards,

Archana
UCSC Genome Bioinformatics Group

Shauna Kanel wrote:
> I forgot to mention, this data is from the same gene in an array of  
> 40 different species that I would like to compare.
>
> Shauna Kanel
>
> Molecular Genetics Division
> Conservation and Research for Endangered Species
> Zoological Society of San Diego
> Phone: 408-892-4566
> Fax:     760-291-5451
> email: skanel at ucsd.edu
>
> _______________________________________________
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