Didn’t find your spanins in the genome? Want to be sure that you didn’t miss any candidates? Try the new toolset designed just for that purpose.
These tools are meant to be used together to help find potential i-spanin/o-spanin pairs. The ISP and OSP candidate tools start with naive gene-calling from an input genomic fasta. All putative proteins are analyzed as long as they have an “ATG”, “TTG”, or “GTG” start codon. Each potential gene is measured against a set of criteria, including TMD distance from the start site for i-spanins, and lipobox presence for o-spanins. The putative_isp and putative_osp gff3 outputs can be routed to Apollo as an evidence track, or the fasta outputs can be fed to the Find Spanin tool to narrow down the candidates list by proximity. The final output is presented based on type: embedded, overlapping, or separate.
These tools written by Curtis Ross are in Galaxy under:
CPT: OTHER– ISP candidates, OSP candidates, Find Spanin
Please email the support team if you have any questions!