How to interpret alignment scores ?

Question

[karakasmenderes6]

Heyy, I am trying to interpret my alignment score but I don"t know how to do this. I had two fasta files and I used Biopyhton two align those and I got a score of 728.0 so what does this mean is it high or low ? if both of them were the same, what would be the score ? My sequence is a nucleotide sequence and I am a newbie in bioinformatics so I hope my question is not inappropriate. My code is below;

from Bio import SeqIO

from Bio import Align

aligner = Align.PairwiseAligner()

hem_1= SeqIO.read("hem_1.fasta", "fasta")

hem_2 = SeqIO.read("hem_2.fasta", "fasta")

score = aligner.score(them_1.seq, hem_2.seq)
print(score)'

[Asaf]

See this thread: Computing statistical cutoff from global pairwise alignment scores

[karakasmenderes6]

I am really thankful, I will read this thread.

[karakasmenderes6]

I am really appreciate. I will examine these links.

Answer 1

[Mensur Dlakic]

Generally speaking, that is a good score. However, alignment scores are length-dependent, so for a really long alignment - say 10 thousand nucleotides - this would not be a good score. You can in fact see what scores these two sequences would get when aligned against the same sequence by putting the same file name in hem_1 and hem_2. That will give you a feel for what a perfect score should be.

Because alignments scores are length-dependent, a better way to assess relatedness between sequences is by using E-values. Asaf already gave you a link that has some info in that regard, and you may want to check this one as well.