NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction

BMC Bioinformatics

Table 1 non-cNLS and cNLS sets

ORF	Gene name	Start	Stop	Necessity or Sufficiency (PMID)	Receptor binding or pathway dependency (PMID)
YBR009C	HHF1	4	21	11694505	11694505^b
YBR010W	HHT1	10	28	11694505	11694505^b
YDL007W	RPT2	11	15	15210724	15210724^a
YDL007W	RPT2	33	37	15210724	15210724^a
YDR103W	STE5	49	66	10481914	10481914^b
YDR146C	SWI5	636	655	7615496/1652372	18485366^a
YDR208W	MSS4	347	364	12912920	12912920^b
YDR224C	HTB1	30	36	3123916	15679097^b
YEL009C	GCN4	231	246	12455686	18485366^a
YER040W	GLN3	388	394	12624103	12624103/18485366^a
YFR034C	PHO4	141	166	9732266	9732266^b
YGL071W	AFT1	202	207	14523005	14523005^b
YGL071W	AFT1	352	355	14523005	14523005^b
YGL071W	AFT1	332	335	14523005	14523005^b
YGL097W	SRM1	3	23	18485366	18485366^a
YHR079C	IRE1	645	657	17035634	17035634^a
YIL075C	RPN2	811	832	15210724	15210724^a
YIL150C	MCM10	512	527	13680157	18984568^a
YIL150C	MCM10	435	451	13680157	18984568^a
YJL194W	CDC6	27	33	18485366	18485366^a
YLR103C	CDC45	209	228	18485366	18485366/18984568^a
YLR182W	SWI6	157	169	14998990	14998990^a
YML007W	YAP1	5	59	11274141	11274141^b
YMR127C	SAS2	19	35	15788653	15788653^b
YMR239C	RNT1	461	466	15090619	15337846^a
YNL027W	CRZ1	394	422	11535618	11535618^b
YNL027W	CRZ1	612	615	11535618	11535618^b
YOL123W	HRP1	522	534	18343812	18343812^b
YOL127W	RPL25	18	28	1920406	9182759/9687515^b
YOL127W	RPL25	11	17	1920406	9182759/9687515^b
YPL153C	RAD53	785	807	15972895	15972895^a
YPR119W	CLB2	183	200	18485366	18485366^a

Characterized yeast nuclear localization signals used in our analysis for which import pathway is known. ^a corresponds to classical NLSs, ^b corresponds NLSs known not to dependent on the classical NLS import pathway. See text for details of how NLSs were classified. Numbers in the last two columns indicate references using pubmed IDs (PMID).

ISSN: 1471-2105