Bioinformatics summary - current status

Species	454 ID	Small RNA sequence count				cDNA targets used
		total data		mapped zero mis-matches		sequence count	sequence source
		reads	distinct	reads	distinct
Maize:	Run # 1	157,944	65,272	108,399	42,887	36,563	ZmGI release 16 TIGR
	Run # 2	119,098	81,719	67,896	43988
Rice:	Run # 1	53,750	25,009	35,486	12,868	62,827	OSA1 release 4 TIGR
	Run # 2	164,623	122,523	121,167	88,481
	RoApx	319,964	185,467	274,648	149,401
	ShApx	303,622	219,754	262,040	183,861
	Infl	429,729	283,688	363,637	229,151
	Leaf	355,902	147,153	261,191	91,105

N.B. In keeping with the predominant notation in the small RNA community, the column formally labeled as 'unique' in the above table is now labelled as 'distinct', and refers to the sequence and not to a map position. That is, the total nucleotide sequences can be reduced to a set of distinct sequences, some of which may be mapped to multiple places within the genome sequence.


Plant small RNAs, which include miRNAs, siRNAs and trans-acting siRNAs (ta-siRNAs), represent a class of regulatory molecule that is increasingly being seen as a significant component of epigenetic processes as well as an important component of gene networks involved in development and in homeostasis. Here we present a bioinformatic resource for cereal crops consisting of large-scale datasets of maize and rice small RNA sequences generated by 454 Life Science sequencing. The small RNA sequences have been mapped to the rice genome and available maize genome sequence and are presented in two genome browser datasets using the Generic Genome Browser (Lincoln Stein). Potential target sequences representing mature mRNA sequences have been predicted using the FASTH software from the Zuker lab. and access to the resulting small RNA target pair (SRTP) dataset has been made available through a mysql based relational database. Within the genome browser the small RNAs have links to the SRTP database that will return a list of potential targets. The SRTP database may also be searched independently using both small RNA and target transcript queries. Data linking and integration is the main focus of this interface and to this aim links are present in the SRTP results pages back to the browser and the SRTP database as well as external sites. The resource will be updated as more sequences become available.