Type of RSS
It is possible to display cryptic RSS with a spacer of 12 bases, or 23 bases, or both 12- and 23-spacer RSS.
The database has been loaded with human and mouse sequence from genome-wide cRSS searches.
Screen results with RIC filter
The results can be filtered using the RIC score. The RIC score goes from -1000 (very bad) to 0 (very good). It has been shown that there is a good correlation between this score and the RSS functionality.
For the current version, pass/fail RIC thresholds are from Cowell et al (2002) as follows:
12 RSS: pass with RIC > -38.81
23 RSS: pass with RIC > -58.45

Literature on RIC filter:
Cowell et al. Computational tools for understanding sequence variability in recombination signals. Immunol Rev.(2004).
Lee et al. A functional analysis of the spacer of v(d)j recombination signal sequences. PLoS Biol.(2003).
Cowell et al. Identification and utilization of arbitrary correlations in models of recombination signal sequences. Genome Biol.(2002).

Chromosomal search
The search has to be restricted to a single Chromosome As an option, the search can be restricted to a specific region of the chromosome:
(a) enter the cytoband,
Example: search for cytoband p12 in the human chromosome 5 , or
(b) enter the base co-ordinates for the chromosome selected(e.g. 10000-20000)
These numbers may contain commas (e.g. 10,000-20,000).
Example: search for region from base 10000 to base 20000 of murine chromosome 7
Gene search in all chromosomes
If this option is selected, the name of the gene entered in the text area is searched and the rss located inside to transcription region are displayed. The region goes from the transcription start to the transcription end of the gene, this region can be expanded upstream and downstream using the menu close to the text area
Example: search for gene LMO2 plus 1000 bases upstream and downstream
Select output format
Two different outputs can be selected: Tab-delimited text or UCSC-uploadable format.
If the tab-delimited text is selected the results will displayed as a table with the different fields separated by a tab.
The results can be selected and pasted into excel. In order to paste the results in excel, select "paste special" from the edit tab. From the different options displayed select text.
If the UCSC-uploadable format option is selected the data will be automatically uploaded to the UCSC genome browser (this may be slow depending on the number of sequences uploaded).
Analyse your own sequence
x or N are not accepted !!!!!
For multiple sequences analysis Only sequences in FASTA format are accepted For single sequence analysis Sequences with or without the FASTA definition line are accepted:
Sequence interspersed with numbers and/or spaces is allowed:
1 atggggatag ggatagacag 20
21 atggggata atggggatag 30
For multiple sequences analysis
More than a sequence can be entered at the same time, for this option the sequence has to be in FASTA format.
Example: analyse two sequences in FASTA format