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RNAcast - Manual
INPUTInput for RNAcast must be provided in a multiple
fasta format, e.g.:
> TMEPP
CACACAAAGGCAGCGGAACCCCCCUCCUGGUAACAGGAGCCUCUG
CGGCCAAAAGCCACGUGGAUAAGAUCCACCUUUGUGUG
> EMCBCG
CCUUUGCAGG CAGCGGAAAU CCCCACCUGG UAACAGGUGCC
UCUGCGGCCA AAAGCCACGU GUAUAAGAUA CACCUGCAAAG G
> MNGPOLY
CCUUUGCAGGCAGCGGAAUCCCCCACCUGGUGACAGGUGCCUCUGCGGCCGAAAGCCACGUGUGUAAGACACACCUGCAAAGG
Newlines and whitespaces are removed from the input. Every
non [a,c,g,u,t,A,C,G,U,T] character is removed from the sequence
data.
The default energy range above the mfe-value is 10 kcal/mol.
Increasing this value results in more common shapes, but also
increases computation time.
RNAcast reports the best k common shapes, where k is a user
defined variable (default is 3). An explanation of abstract shape
mappings can be found in the RNAshapes manual.
OUTPUTThe output of RNAcast first shows the common
shape, the achieved score and the ratio of the achieved score and
the sum of all mfe values. A ratio near 1.0 means a good
conservation, a lower ratio means less conservation. Thereafter,
for each input RNA and not aligned, there is the sequence, the
predicted shrep, its energy, and its individual rank in the shape
space.
Shape #1: [[][][]] Score: -107.41 Ratio of MFE 0.99
> TMEPP
CACACAAAGGCAGCGGAACCCCCCUCCUGGUAACAGGAGCCUCUGCGGCCAAAAGCCACGUGGAUAAGAUCCACCUUUGUGUG
(((((((((((((.((.......((((((....)))))))).))))(((.....)))..((((((...))))))))))))))) (-33.71) R = 2
> FDI251473
GCACGCAAGCCGCGGGAACUCCCCCUUGGUAACAAGGACCCGCGGGGCCGAAAGCCACGUUCUCUGAACCUUGCGUGU
((((((((((((((((.......(((((....))))).)))))))(((.....)))..((((...))))))))))))) (-34.10) R = 2
> PIFMDV2
GCAUGUUGGCCGUGGGAACACCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCAUGUCCUAACGGACCCAACAUGU
((((((((((((((((......((((((....)))))))))))))(((.....)))..((((....))))))))))))) (-39.60) R = 1
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