Lowe Lab
 Snoscan Server 1.0 		[UCSC]
Search for C/D box methylation guide snoRNA genes in a genomic sequence
Snoscan is based on an algorithm described in:
     Lowe, T.M. & Eddy, S.E. (1999) "A computational screen for methylation guide snoRNAs in yeast", Science 283:1168-71

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

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

You may also wish to refer to the Eddy/Lowe snoRNA Database of methylation guide snoRNAs for yeast & Archaeal snoRNAs.

Probabilistic Search Model:



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)
Sample yeast snoRNA sequences

OR submit a file:



Show results in this browser, OR
Receive results by e-mail instead:
  




Target RNA Sequence (e.g. rRNA)

Format:

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

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

Paste your target RNA sequence(s) here:

(The web-server may experience problems if submitted targets total more than 10K nucleotides at any one time)

OR submit a file:

OR use a provided target RNA sequence:




Optional: Specify positions of known or predicted sites of methylation

Methylation file: 

Methylation file format | Yeast methylation file | Human methylation file

Filtering / Sorting Options:  (Default: sort all hits by overall score)

Sort hits by: Filter hits by target site:

Output only top hits per methylation site

Simplify output information

Search Options:

Final Score cutoff:  C Box Score cutoff: 
Minimum length for snoRNA-rRNA pairing:  D' Box Score cutoff: 
Minimum score for complementary region:  Max distance between C and D boxes: 
Initiate scan at this position in sequence:  Max distance to known methsite: 
Min distance between rRNA match and Dbox when D'box is present: 

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


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