The remnant effect terms are mapped to unknown processes in CSML, though they will be converted with a similar methodology described in this section.
To reduce the influence of noise data, we also remove the duplicated interactions, self interactions and interactions associated with proteins that are functionally unknown or cannot be mapped to UniProtKB/Swiss-Prot entries.
Because the kind of process that is inhibited is not explicitly stated in TP, this reaction is mapped to an unknown process.
The comparison of the genetic map positions of these 3 loci (Additional file 3) and the previously identified dnf mutants (D. Wang, personal communication) suggested that either the mutant loci 5L/11S, 7Y and 13U are mapped to genomic locations with unknown symbiosis genes or the known symbiotic locus in the corresponding region was not allelic (13U and dnf2; [ 22]).
The 50-bp reads (query reads) obtained from Frankia genomes of unknown sequence (query genomes) were mapped to a reference genome whose complete sequence had already been reported [ 4] — Frankia strains ACN14a (GenBank: NC_008278.1), CcI3 (NC_007777.1), and EAN1pec (NC_009921.1).
In order to identify unknown gene reads, SOLiD cDNA reads were mapped to the Roche 454 reads.
A mutant with reduced sensitivity to Smex was mapped to the OXOPROLINASE1 locus, while a mutant with enhanced sensitivity to Smex mapped to a gene of unknown function.
Furthermore, potential novel miRNAs mapped to unknown contigs not associated with any of the three A. gambaie chromosomes, with multiple and inexactly mapped reads were filtered out.
Neves et al. (2013) showed that this advantage is of greater importance for a segregating population because even if previously characterized polymorphisms are available, the sites that will segregate in a single biparental segregating population and have potential to be mapped are unknown.
We show that with the current sequencing technologies and DNA capture approaches unknown mutations can be mapped robustly to a single genomic region.
