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