Local or global alignment for gene fragments?

Peter Frank peter_frankde at yahoo.de
Tue Jun 17 01:12:56 EST 2003

I got gene fragments of different lengths from cDNA libraries and
would like to perform pairwise alignments with selected matches which
I got from BLAST searches.

Should I use local or global alignment algorithms for these pairwise
alignments? The percentage of how much the gene fragments make up of
the complete genes (= BLAST search results) varies widely.


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