FrameAlign creates
an optimal alignment of the best segment of similarity (local alignment)
between a protein sequence and the codons in all possible reading frames on a
single strand of a nucleotide sequence. Optimal alignments may include reading
frame shifts.
Pairwise Comparsion
Query:Nucleotide sequence
Against:Protein sequence
3 GAAATCAAGAAGGCCATCAAGGAGGAATCTGAAGGCAAAATGAAGGGAAT 52
|||||||||||||||||||||||||||||||||||||||:::||||||||
261
GluIleLysLysAlaIleLysGluGluSerGluGlyLysLeuLysGlyIl 277
.
.
.
.
.
53 TTTGGGATACTCTGAGGATGATGTTGTGTCTACCGACTTTGTTGGTGACA 102
||||||||||...|||||||||||||||||||||||||||||||||||||
278
eLeuGlyTyrThrGluAspAspValValSerThrAspPheValGlyAspA 294
.
.
.
.
.
103 ACAGGTCAAGCATTTTCGATGCCAAGGCTGGATTGCATTGCATTGAGCGA 152
|||||||||||||||||||||||||||||||| ||||||||||||||
295
snArgSerSerIlePheAspAlaLysAlaGly....IleAlaLeuSerAs 309
FrameAlign always
finds an alignment for any protein and nucleotide sequences you compare, even if there is no significant similarity between them.
You must evaluate the
results critically to decide if the segment shown is not just a random region of relative similarity