Argo User Guide: Scientific Scenario

In a study characterizing cell adhesion molecules encoded by the genome of Ciona savignyi (super_15687.fa), high scoring tblastn hits were detected in the contig sc15687 using human integrin α subunits as query sequence (sc15687_huints_tbn.out). Examination of GenomeScan and GENSCAN gene predictions from this contig (sc15687.geos and sc15687.gs, respectively) revealed a gene that encoded a protein with an unusual molecular architecture. jAs shown below, the ab initio prediction appears to be a concatenation of two integrin proteins:

Typical human integrin α subunit:

human integrin subunit

GenomeScan predicted peptide:

GenomeScan predicted peptide

Credit: Thanks to Charlie Whittaker (MIT) for creating this use case.


Last Updated: Sept 18 2006
Contact: Reinhard Engels
argo-support@broad.mit.edu