Bioinformatics summary - current status

Species 454 ID Small RNA sequence count cDNA targets used
total data mapped
zero mis-matches
reads distinct reads distinct
Run # 1 157,944 65,272 108,399 42,887 36,563 ZmGI
release 16
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
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.