Tool for SNP detection between two DNA sequence?

Question

[mbk0asis]

Hi

I'm looking for a tool to detect SNPs between DNA sequences.

For example, when I enter input sequences

seq1 = GATC
seq2 = GTTC

The result should contain the base position (2nd base in this case) and will be better if mutated bases also appears (A/T).

I've been looking for a software, but no luck yet.

Someone might say I can just code for it, but my coding skill doesn't reach the level.

Beside, I'm sure somebody already made one.

So if anyone knows it, please let me know.

Thank you!

Answer 1

[Pierre Lindenbaum]

I wrote a tool to extract the variation from a BlastN+XML input. See Find Mismatch And Gap Positions and https://github.com/lindenb/jvarkit/wiki/BlastnToSnp

[mbk0asis]

Thank you, Pierre!

I really wanted to try the tool you made, but I don't really understand how to compile it.

I followed the instruction on the jvarkit page. No success yet.

Would you please explain the compilation process?

[Pierre Lindenbaum]

please tell me what's going wrong.

[mbk0asis]

Sorry to bother you. I figured out. Java was 1.7 and ANT wasn't in my system. Sorry again.

[h.mon]

There is another tool on Pierre's Github which may suit your needs, found it on this thread.