Information on Multiple Sequence Alignment Program

The MAP program computes a multiple global alignment of sequences using iterative pairwise method. The underlying algorithm for aligning two sequences computes a best overlapping alignment bewteen two sequences without penalizing terminal gaps. In addition, long internal gaps in short sequences are not heavily penalized. So MAP is good at producing an alignment where there are long terminal or internal gaps in some sequences. The MAP program is designed in a space-efficient manner, so long sequences can be aligned. Note that sequences must be all DNA/cDNA sequences or all protein sequences.

NOTE: If the computation takes more than a few minutes, we suggest that the user obtain results via email by choosing the email option and providing an email address. Otherwise, an error may occur due to connection timeout.

Huang, X. (1994) On Global Sequence Alignment. Computer Applications in the Biosciences 10, 227-235.

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Please contact Xiaoqiu Huang at xqhuang@cs.iastate.edu