sORFfinder is a web-based tool to identify small open reading frames (sORF) with high coding potential. However, web-application has some limitations. You can conduct more sophisticated analysis in your local compute downloading the perl scripts. The limitation of web-application is written in the methods. Web-based program has two applications. First, you can identify sORFs which have similar nucleotide composition of coding genes by hiden markov model (Search_sORF). Then, the functionality of sORFs can be examined by comparative genomics (Examine_SP). Please see Application Note of this program package published in Bioinformatics.

  1. Search_sORF can identify small open reading frames (sORF) with coding potential by hiden markov model
    Web-application had already prepared studying models of 11 species (S.cerecisiae, A.thaliana, O.sative, C.elegans, D.melanogaster, A.gambiae, C.intestinalis, X.laevis, D.rerio, G.gallus and H.sapiens). You should choose one of studying model from 11 species. Using the selected model, you can search sORF wiht high coding potential. However, if you want to use studying model for other organisms, you need to conduct the analysis in your local computer.

  2. Examine_SP can infer functionality of identified sORF by comparative genomics. First, this program searches homologous sequences from available EST or genomic sequences and calculated synonymous (without amino acid replacements) and non-synonymous (with amino acid replacements) nucleotide substitutions. If sORF is functional, it is likely that synonymous substitutions have occurred more frequently than non-synonymous substitutions. Finally, in each sORF, you can get P-values which can be indicatorl for functionality.

Please send e-mail to me if you have problems or errors.

Kousuke Hanada

RIKEN, Plant Science Center

E-mail: kohanda (at) psc (dot) riken (dot) jp