TransposonPSI is an analysis tool to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements. PSI-Blast is used with a collection of (retro-)transposon ORF homology profiles to identify statistically significant alignments.
This method can be used to identify potential transposon ORFs within a protein set, or to identify regions of transposon homology within a larger genome sequence. This is particularly useful to identify degenerate transposon homologies within genome sequences that escape identification and masking by using RepeatMasker and an associated nucleotide library of repetitive elements.
TransposonPSI has been routinely used at The Institute for Genomic Research to assist in the discovery of mobile elements across eukaryotes including protozoa, plants, fungi, and animals.
· NCBI blast, including blastall and blastpgp