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Analyses
(1993)]. BLOSUM tables have proven to be more accurate than projecting
similarities of distantly related proteins based on known similarities of closely
related proteins, which is how the PAM matrices were developed. In general,
it is best to start off using a BLOSUM62 matrix for your comparisons. As with
the PAM tables, the closer related the sequences are the lower value BLOSUM table you should use. Sequences that are more distantly related should
be compared using higher value BLOSUM tables.
The output from this alignment is shown in Figure 4.48. In this instance,
Figure 4.48: Global Sequence Alignment
alignment indicators are shown and indicate regions of highest similarity.
Align Multiple Sequences
The parameters for this analysis are similar to those in the section on multiple
sequence alignments in nucleic acid sequences (page 4-20) and are discussed in detail in “Multiple Sequence Alignments”, page 3-10. The only difference between running a multiple sequence alignment as a sequence
analysis (Analysis ?New analysis…) and initiating the multiple sequence alignment
within a sequence editor is the way in which you are allowed to choose
sequences for the analysis. Doing a multiple sequence alignment as an analysis will let you choose to align any number of sequences from any number
of sequence files. Running the alignment from within the sequence editor only
works on the entire set of sequences in the sequence editor document – you
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