Researchers have introduced POASTA, a new algorithm for partial order alignment that significantly improves the efficiency and accuracy of sequence alignment. POASTA, written in Rust, leverages gap-affine partial order alignment to handle long stretches of matching sequences between a graph and a query. The algorithm utilizes the A* algorithm and depth-first search components to accelerate alignment, and includes methods to detect and prune non-optimal alignment states. This innovation allows for the construction of much larger partial order alignment (POA) graphs than previously possible, enabling megabase-length alignments of sequences, such as the alignment of 342 Mycobacterium tuberculosis (Mtb) sequences. Additionally, POASTA doubles sensitivity to remote homologs by using large protein structure alphabets.
POASTA accelerates alignment using the A* algorithm, a depth-first search component, greedily aligning exact matches b/n the query and the graph; and a method to detect and prune alignment states that are not part of the optimal solution, informed by the POA graph topology.
POASTA's algorithm is based on an alignment graph, enabling the use of common graph traversal algorithms such as the A* algorithm to compute alignments. POASTA enables the construction of megabase-length POA graphs.
POASTA: Fast and exact gap-affine partial order alignment https://t.co/SX1bnTZviq https://t.co/195kmGivEO
"We present POASTA, a new optimal algorithm for partial order alignment that exploits long stretches of matching sequence between the graph and a query.... construction of much larger POA graphs than previously possible....megabase-length alignments of 342 Mtb sequences" https://t.co/wizrmBvi13
So cool; and written in Rust! Fast and exact gap-affine partial order alignment with POASTA https://t.co/Ohf3G0INOh
Fast and exact gap-affine partial order alignment with POASTA https://t.co/xOI5j85N6u #biorxiv_bioinfo
Sequence alignment using large protein structure alphabets doubles sensitivity to remote homologs https://t.co/IPBEodk4jm #biorxiv_bioinfo