Align sequences, multiplying

While the information contained in one primary sequence alone seems to be insufficient to predict a protein s secondary structure, multiply aligned sequences (see below) offer a means to push the limits of the prediction. Originally due to Zvelebil et al. [26] this line of attack on the problem is the basis of the PHD method by Rost and Sander [27]. The PHD method takes as input a multiple alignment of a set of homologous protein sequences and... 

ALSCRIPT provides a few commands for calculating residue conservation across a family of sequences and coloring the alignment accordingly. However, it is really intended as a display tool for multiple alignments rather than an analysis tool. In contrast, AMAS (Analysis of Multiply Aligned Sequences Livingstone and Barton,... 

Mehta, P. K., Heringa, J., and Argos, P. (1995). A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%. Protein Sci. 4, 2517-2525. 

BLOCKS [22,23] is an automatically generated protein family database closely related to PRINTS like the latter, it represents patterns characterizing family membership as sets of multiply aligned, ungapped sequence segments (BLOCKS). 

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