Sequence alignment plays a significant role in many bioinformatics problems, primarily as a means of detecting and quantifying evolutionary similarity. In the special case where an amino acid sequence is aligned to a protein structure, we often use the term threading, which suggests pulling a flexible string through the backbone of a 3-dimensional template. Most programs currently treat the query sequence, the template, or both, as a position specific scoring matrix (PSSM). A PSSM can be computed from a multiple sequence alignment (MSA). However, since there is a loss of information in the conversion of an MSA to a PSSM (many different MSAs will yield the same PSSM), MSThread treats the query MSA directly.

The query MSA is prepared using the program MAFFT. Each template MSA is pre-computed using the program MAFFTash.

A manuscript describing the MSThread method is currently in preparation (A. Han, et al.), but the source code for the core algorithm can be downloaded here.

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