Introduction to AlignMe

AlignMe is a program that allows the user to perform pair-wise alignments for

• two sequences,
• two multiple sequence alignments, or
• two profiles.

The similarity (Sim(i,j)) between two amino acids (i and j) may be measured by their evolutionary relationship in terms of a substitution matrix (S(a,b)) or by differences of biochemical profiles, such as hydrophobicity or predicted structural values, computed as (|V(a) – V(b)|). AlignMe can combine any number of input profiles (n) with any number of input substitution matrices (m) and can use different weights (w) to guide the combination of those inputs in generating the alignment.

This similarity measure is calculated for all amino acid pairs of two sequences in the Needleman-Wunsch algorithm. Additionally the user can choose between several gap penalty schemes for the treatment of mismatching stretches.

In all modes of usage, the user has to provide two files, one for each of the sequences, and a so-called similarity-score file, which contains the user-defined combination of inputs that will be used to compute the similarity scores.

The user can also define any number of constraints or anchors. The anchors can be tuned in strength from preference to enforcement.

For more information see: Stamm, M, Staritzbichler, R, Khafizov, K, and LR Forrest. 2013 “Alignment of Helical Membrane Protein Sequences Using AlignMe” PloS One 8 (3):e57731