In bioinformatics and proteomics, ProbCons is an open source software for probabilistic consistency-based multiple alignment of amino acid sequences. It is one of the most efficient protein multiple sequence alignment programs, since it has repeatedly demonstrated a statistically significant advantage in accuracy over similar tools, including Clustal and MAFFT.

Algorithm

The following describes the basic outline of the ProbCons algorithm.

Step 1: Reliability of an alignment edge

an alignment that is generated by the model.

are in the alignment and 0 otherwise.)

Step 2: Maximum expected accuracy

is defined as the number of common aligned pairs divided by the length of the shorter sequence.

Calculate expected accuracy of each sequence:

This yields a maximum expected accuracy (MEA) alignment:

Step 3: Probabilistic Consistency Transformation

are now re-estimated using all intermediate sequences z:

This step can be iterated.

Step 4: Computation of guide tree

Construct a guide tree by hierarchical clustering using MEA score as sequence similarity score. Cluster similarity is defined using weighted average over pairwise sequence similarity.

Step 5: Compute MSA

Finally compute the MSA using progressive alignment or iterative alignment.

See also

• Sequence alignment software

• Clustal

• MUSCLE

• AMAP

• T-Coffee

• Probalign

References

External links