FSHIFT

Fshift is a dynamic programming sequence alignment algorithm that explicitly incorporates frameshifts in a biologically realistic manner. The program takes a protein query sequence and compares it with a translated DNA library sequence. The translated DNA library sequence is examined in the three forward reading frames, looking for a frame-shifts that are primarily due to laboratory sequencing errors. The protein alignment presented is allowed to jump from frame to frame at the cost of a penalty that reflects the infrequency of frameshift mutations.

Installed on the Opteron Cluster.

Fshift documentation

• User's Manual

See Also:

• Other nucleic acid and protein sequence analysis software installed at the PSC.