Molecular Genome Analysis

3 of 5


Purpose Formats Syntax


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The 3of5 application aims at the analysis of protein sequences to find user-defined patterns. The peptide patterns can be described via regular expressions-like terms.

Both, query sequences as well as patterns are chosen and imported by the user. Different input formats are available.

3of5 offers new features in peptide pattern searches:

(1) The n-of-m pattern type allows for the definition of ambiguities in patterns, where individual elements may vary in position, order and content. This n-of-m pattern type can be combined with common regular expressions and thus allows for the description of complex patterns. In addition, an excluded set may be defined listing such characters that are not allowed to be contained within the specified pattern. Furthermore there is an extended syntax of 3of5 to describe a peptide pattern even more specifically: Numerical constraints can be set and applied to different characters or groups of characters. The name 3of5 has its origin in a special use of this main feature n-of-m (part of the nucleoplasmin nuclear localisation pattern).

(2) 3of5 finds ALL possible solutions in case of length-ambiguous peptide patterns, instead of reporting only the longest or shortest hits.

(3) Grouping of patterns via the FASTA grouped mode provides a hierarchical arrangement of patterns sets and facilitates a structured display of the results.