Biocomputational prediction of small non-coding RNAs in Streptomyces

BMC Genomics

Table 2 Streptomyces sRNAs predicted using an alternative transcription termination.

ID#	Exp.†	Length	Strand*	Genomic coordinates	E-value	5'-flanking gene distance	5' flanking gene termination#	RNAz probability @
60	++	252	← ⇒ →	7243744.. 7243995	2 × 10^-74	17		0.99
544, M1 RNA	++	320	← ⇐ ←	2462901..2463220	9 × 10^-94	2	C-rich, 2463157.. 2463177	1

† The first symbol stands for detection of expression by microarrays (expressed: '+', not expressed: '-'), the second one for RT-PCR confirmation of the expression (expressed: '+', not expressed: '-'). '0' stands for not applied.
* The double arrows represent sRNA gene, the arrows flanking genes. Right sided arrows show the complementary strand.
# Applicable only if the predicted sRNA and the gene flanking its 5' end are on the same strand. 'C-rich' stands for C-rich stretch of possible Rho-dependent transcrition termination. 'Rho-ind.' stands for a predicted Rho-independent terminator. The number following show the genomic coordinates of the termination factors.
@ In alignments with P < 0.5 a functional RNA is predicted. The higher this value, the more confident is the prediction.

ISSN: 1471-2164