Want to know whether motif finding is Multiple Sequence Alignment technique. And I want references about motif finding and Multiple Sequence Alignment
Read the ten simple rules. Link is at the very top.
Motif finding doesn't necessarily need of multiple sequence alignment, just to find profiles of short stretches of nucleotides (e.g. form 6-14) that are seen over and over in a list of sequences. One of the ways of getting some of these motifs is to compare them across species, and look at the ones that are conserved among them. In those cases, a multiple alignment for the genome of those species is used.