Detailed local genomic sequence analyses reveal new patterns of expanded microRNA families (hsa-mir-1233). Typical Ensembl sequence alignment picture reveals that novel paralogs will not be found if using only segmental duplication analysis, since it will detect only > 1 kb fragments of > 90% identity. In the region around 200–258 bp corresponding to conserved sequences to two microRNAs (in red frame), hsa-mir1233-1 and hsa-mir1233-2 (100% identity as indicated), we can see multiple genomic fragments, which are short and isolated, but highly conserved (percentage of identity can be found in Additional file 2). These genomic regions could contain potential microRNA paralogs. HSPs = high scoring pairs.
Du et al. BMC Genomics 2013 14:98 doi:10.1186/1471-2164-14-98