What is the typical size of the sequence files while conducting pairwise sequence alignments?

StackOverflow https://stackoverflow.com/questions/22890769

Question

What is the typical size of the sequence files while conducting pairwise sequence alignments? Can we align the whole genome of organisms?

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Solution

There are two types of pairwise sequence alignments, local and global.

Local pairwise alignment is trying to locate only parts of two sequences that are similar. There is not a typical sequence size since there is a huge variation. For humans it is 10-15kb (10000-15000 base pairs), according to this: http://bionumbers.hms.harvard.edu/bionumber.aspx?&id=104316&ver=1 .

In the case of global alignment, we attempt to align all the residues of the two sequences. Using global alignment methods, we can align the whole genome of organisms but this has some use only in the case of closely related organisms, where the genome has not diverged a lot. For an example of how it can be done, see this: http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto

Also, this describes multiple whole genome alignments which can be more useful: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157923/

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