Lowe Lab
 snoGPS Server 		[UCSC]
Search for H/ACA snoRNA genes in a genomic sequence

snoGPS 1.0

The principles underlying the snoGPS program are described in:
    Schattner P, Decatur WA,  Davis C,  Ares, M,  Fournier, MJ and Lowe, TM, (2004)
     "Genome-wide Searching for Pseudouridylation Guide snoRNAs: Analysis of the
     Saccharomyces cerevisiae genome”, Nucleic Acids Res vol. 32(14): pp. 4281-4296

Instructions for using the snoGPS server and interpreting the output can be found in the snoGPS README file.

If you would like to run snoGPS locally, you can get the UNIX source code (gzipped tar file).


Source:
Scanner:
Two stem
One stem

Query Sequence

Format:

Raw Sequence
Sequence name (optional): (no spaces)

Other (FASTA, GenBank, EMBL, GCG, IG)

Paste your query sequence(s) here:

(The web-server may experience problems if submitted queries total more than 100K nucleotides at any one time)
or submit a file:

To try out the server, you can use this sample human H/ACA snoRNA sequence.

Target Sequence

Choose a target sequence:

...OR input your own sequence.

Format:

Raw Sequence
Sequence name (optional): (no spaces)

Other (FASTA, GenBank, EMBL, GCG, IG)

Paste your target sequence(s) here:

(The web-server may experience problems if submitted queries total more than 100K nucleotides at any one time)
or submit a file:
Enter your own pseudouridine file: 
Show results in this browser.
Receive results by e-mail instead:

Output Sorting Options:

Sorting method: Output only top hits per pseudoU site

Remove lower-scoring overlapping candidates Check positive strand only Guide region score cutoff: 
Final Score cutoff: 

Send comments/questions/problems using this search page or local installation of snoGPS to schattner@soe.ucsc.edu


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