What does the output mean by using spaln -O1 option
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Hi ogotoh,
Recently, I used spaln to align aa sequence to DNA sequence by using the parameter -O1.I don't understand about the output "Score = 4091.0 (1174.1), 40.0 (=), 122.0 (#), 8.0 (g), 12.0 (u), (22.99 %)"means. Would you please help me about what does these numbers mean? Thanks a lot!
I wonder your alignment was not successful because the two score values differ too much. Please refer to my comments in issue #19. Or you are trying intrinsically difficult alignment.
The first line indicates parameters used for alignment:
PAM: PAM level of Dayhoff’s style amino-acid substitution matrix. (by default spaln uses JTT matrix).
BIAS: If != 0, this value is added to the above substitution matrix. Adjustable with –yb_N_ option.
u: Gap extension penalty.
v: Gap open penalty.
The second line:
Score = Raw (Modified): alignment scores. Modified score takes account the number of inferred exons. Otherwise, intron-less processed pseudogenes might give better row score than the true gene.
M (=): Number of identical residues between the query and (translated) genomic sequence.
N (#): Number of mismatched residues between the query and (translated) genomic sequence.
G (g): Number of gaps in the alignment after splicing.
U (u) Number of unpaired (either being a space) residues in the alignment after splicing.
(P %) Percent of identically matched sites in the alignment = 100*M/(M+N+G).
The third line:
A delineator indicating that the real alignment starts after this line.
Thanks very much about your comment, I also have another question. Can I just treat the (=)number as the tblastn output Identities&Positives number or just the Indentities number between query and the translated genomic sequence?
Thank you very much. I have sorted it out.