Bioinformatics summary - current status update
| Species |
454 ID |
Small RNA sequence count |
cDNA targets used |
total
454
reads |
extracted
and
accepted |
mapped
zero mis-matches |
sequence
count |
sequence
source |
| total |
distinct |
Maize:
update |
Run # 1 |
227,710 |
157,944 |
108,399* |
42,887* |
36,563 |
ZmGI
release 16
TIGR |
| Run # 2 |
162,292 |
119,098 |
67,896* |
43988* |
| Rice: |
Run # 1 |
92,298 |
53,750 |
35,486 |
12,868 |
62,827 |
OSA1
release 4
TIGR |
| Run # 2 |
202,504 |
164,623 |
121,167 |
88,481 |
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 (GMOD - 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.