Calculate melting temperature for BLAST output (DNA duplexes with mismatches and gaps)

Question

[stoptime_armstrong]

I know there are a lot of methods to estimate the Tm of a sequence with mismatches and gaps.

I've been using biopython and getting negative values for the addition of gaps. I'm not sure if there is a better tool out there that can calculate Tm for the results of blastn

I would have two strings, query and subject, and blastn always aligns them for you so they are the same length.

Q: ATGCGTGCGTAAAATGCGT
   |||.|||.||||..||..|
S: ATGTGTGTGTAA--TGTTT

I don't want to naively take the mean of the two sequences, rather the Tm of the duplex. Thanks in advance

Answer 1

[Mensur Dlakic]

I know there are a lot of methods to estimate the Tm of a sequence with mismatches and gaps.

I don't know a single method that can do this reliably, and would appreciate if you post links to the methods you know.

I can see all kinds of problems in calculating these melting temperature. Gaps are not the same as mismatches, and two mismatches next to each other are not the same as two mismatches separated by 10 nucleotides. A double gap is not the same as two individual gaps separated by some distance.

I'd be really curious to hear about a method that can predict this reliably.