Alignment and mapping

Question

[statfa]

Hi,

My question may seem so simple. Could you tell me what is the difference between aligning and mapping the short reads to the reference genome?

And also what is the difference between Pairwise alignment, Multiple sequence alignment and Short-Read Sequence Alignment?

Thanks

[GouthamAtla]

Did you try to find the answer in google first ?

[statfa]

yes I'm reading some articles but once they say alignment then the say mapping... I'm getting confused... sorry if my questions seem silly

[Devon Ryan]

I'm not surprised that you're getting confused, it's only in the last year or so that people have started nicely discriminating between the two.

[statfa]

Yeah, thank you very much for your help

[GouthamAtla]

Its not silly. Interesting question. Adding the point "once they say alignment then the say mapping" to the original question would help people to understand that you have tried to find the answer.

Answer 1

[Devon Ryan]

This turns out to be not so simple, so excellent question!

When we align a read, we're asking for not just where it likely came in the genome, but the exact base to base correspondence. For example, we'd like to get something like, "Read foo likely originated from chr1 positions 123 through 140. The first 7 bases are exact matches between foo and the reference, there's then a 3 base insertion, then the remaining bases match between foo and the reference."

When we map a read, we're just asking, "where did it come from?" We don't necessarily care about the exact alignment between the read and where it came from, though.

Until recently, "alignment" and "mapping" were pretty much synonymous. Tools like Kallisto and Salmon have changed that, since they can assign reads to genes/features/whatever without needing to look at exact alignments. Since (A) this is faster and (B) we often don't actually care about the alignment, this is a HUGE advantage in some applications.

[firestar]

For mapping, when you say "we're just asking, "where did it come from?" We don't necessarily care about the exact alignment", how do you know where it came from if you don't align it? ie; You have to check the query bases to the reference bases to know, right?

[statfa]

Thanks a lot for your assistance

[Brian Bushnell]

If you feel a response conclusively answers your question (as this one does, in my opinion), I encourage you to click on "accept". This indicates to others browsing the posts that the question has an accepted answer, which is helpful for everyone.

[statfa]

Oh Ok... Sure... Thank you

[li.anlin666]

Sorry, I can't understand this < "there's then a 3 base insertion, then the remaining bases match between foo and the reference." what happened with the remaining bases? what can imply from the remaining bases? what is the meaning of 3 base insertion? I have so many question .

Answer 2

[Benn]

For your second question, pairwise alignment (e.g., Smith and Waterman) is between two sequences and multiple sequence alignment between more than 2 sequences (e.g., clustalW). Short read aligners are usually pairwise!

[statfa]

Thanks a lot for your assistance