However, to analyse complete sets of multiple protein peaks, more sophisticated statistical methods are required.
Malin provides a graphical user interface for various tasks commonly used to infer the evolution of exon intron structure in multiple protein-coding ortholog sets (Fig. 1) along a fixed species phylogeny.
Thus, we converted the accession numbers in the database to gene names (symbols) and removed the redundancy of gene names that resulted from multiple protein isoforms in each proteome set.
For each set of homologs, a multiple protein sequence alignment was reconstructed using MUSCLE [ 48].
In the second iteration, pairs of MSAs are compared using the Comparison of Multiple Protein Alignments with Assessment of Statistical Significance (COMPASS) set of tools [24].
Genes encoding multiple ribosomal protein subunits, multiple protein translation initiation factors, and translation elongation factors were all found in this AmCDUnigene set.
If there are multiple protein identifiers then there may be ambiguity if they do not correspond to the same set of genes.
All time estimates were calculated with a Bayesian local clock approach [ 97] utilizing concatenated data sets of multiple proteins and a JTT+gamma model of substitution [ 19, 98, 99].
Well-characterized sets of variant forms of multiple proteins are needed to help drive the development of such methods.
We employed GPE in analyzing a glycopeptide data set that contains ETD data of 77 distinct glycopeptides generated from multiple proteins (fetuin, IgG, HIV gp140, etc).
