Realignment Methods

Realigners based on horizontal partitioning

Split an alignment into groups of whole sequences, which are then merged together by realigning between groups, possibly using each group’s induced subalignment.

1. ReAligner (1997)

In each iteration has a traversal of all sequence:

1. Pick a sequence

2. Realign the sequence with the profile constructed with the remaining sequences.

3. If the new alignment's quality is improved, the new one will replace the old one.

Until the alignment score saturates to a stable value.

• Test data: DNA/RNA

• The source code link is unavailable.

2. Remove First method (2005)

In each iteration:

1. Randomly pick a sequence.

2. Realign the sequence with the profile constructed with the remaining sequences.

3. Update the alignment if the accuracy improved.

Until the score converges or the reach the limit of iterations.

• Test data: Protein (HOMSTRAD)

• Source code

3. TreeRefiner (2005)

This realigner is based on three-dimensional alignment rather than using an iterative approach.

• Test data: Nucleotide sequences that were generated by the Rose program

• TreeRefiner's homepage

4. REFINER (2006)

This realigner is similar to RF method but aims to realign the sequences with the family block models representing conserved sequence/structure regions.

In each iteration:

1. Randomly pick a sequence.

2. Realign the sequence with the PSSM constructed with the remaining sequences.

3. Update the alignment.

Until the alignment score saturates to a stable value or until the iteration cycle terminates.

• Test data: Protein (CDD and PFAM)

• FTP server

5. ReformAlign (2014)

In each iteration:

1. Build a profile from the initial alignment.

2. All sequences realign with the profile to obtain the reformed alignment. (There has a profile fine-tuning model.)

3. The alignment with better quality will be the input of next iteration.

Until the alignment between two successive runs remains unchanged or a predefined maximum number of iterations is reached.

• Test data: DNA/RNA (BRAliBase 2.1 RNA alignment database and DNA SMART database)

• ReformAlign's homepage

Realigners based on vertical partitioning

Realigners based on vertical and horizontal partitioning

Realignment in MSA tools

Vertical-oriented realignment in MSA tools

Horizontal-oriented realignment in MSA tools