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Sequence analysis includes a very wide range of relevant topics:
The comparison of sequences in order to find similarity, often to infer if they are related (homologous)
Identification of intrinsic features of the sequence such as active sites, post translational modification sites,gene-structures, reading frames, distributions of introns and exons and regulatory elements.
Identification of sequence differences and variations such as point mutations and single nucleotide polymorphism (SNP) in order to get the genetic marker.
Revealing the evolution and genetic diversity of sequences and organisms
Identification of molecular structure from sequence alone