BALSA Pairwise Sequence Alignment User Manual

1          Sequences

These are the query (R1) and comparison (R2) sequences which the user wishes to align.

 

 NOTE: All sequences must be in FASTA format.

 

2          Scoring Matrices and Gap Penalties

The algorithm assumes that scoring matrices and gap penalties are viewed as pairs.  Additionally, the number of scoring matrices and gap penalty pairs is limited to 4 in the software as little gain in sensitivity is viewed beyond this number and this limitation reduces and the overall computation time.

 

3          3D –Alignment

The algorithm returns the posterior alignment distribution.  This 3-dimensional graph has the positions of the query and database sequences along the x-axis and y-axis.  The probability of residue i on the query sequence aligning with residue j on the database sequence is on the z-axis, P(Residue i , Residue j) in the query and comparison sequences, respectively.

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4          Output

The user has the choice to obtain the output on screen or via e-mail.  The on-screen option will return the Posterior Probability for each scoring matrix/gap penalty combination, Posterior Alignment Distribution, and the Bayesian P-Value. 

 

Example:

> seq 1

> seq 2

P(BLOSUM 45, Gap Opening Penalty = -12, Gap Extension Penalty = -1 | R1, R2) =

P(BLOSUM 50, Gap Opening Penalty = -12, Gap Extension Penalty = -2 | R1, R2) =

P(BLOSUM 62, Gap Opening Penalty = -10, Gap Extension Penalty = -1 | R1, R2) =

P(BLOSUM 62, Gap Opening Penalty = -12, Gap Extension Penalty = -1 | R1, R2) =

 

3D Histogram of P(A|R1, R2}

 

Bayesian p-value() =

 

The e-mail option will return via e-mail the following

 

> seq 1

> seq 2

P(BLOSUM 45, Gap Opening Penalty = -12, Gap Extension Penalty = -1 | R1, R2) =

P(BLOSUM 50, Gap Opening Penalty = -12, Gap Extension Penalty = -2 | R1, R2) =

P(BLOSUM 62, Gap Opening Penalty = -10, Gap Extension Penalty = -1 | R1, R2) =

P(BLOSUM 62, Gap Opening Penalty = -12, Gap Extension Penalty = -1 | R1, R2) =

 

Bayesian p-value() =

 

NOTE:  When using the e-mail option the user will not get the posterior alignment distribution.

 

5          References

  1. Brenner S, Chothia C, and Hubbard TJP. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl Acad. Sci. USA, 95, 6073-6078.

 

  1. Webb BM, Liu JS, and Lawrence CE. (2002) BALSA: Bayesian Algorithm for Local Sequence Alignment.  Nucleic Acids Research, 30:5, 1268-1277.

 

  1. Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, and Brenner SE. (2002) ASTRAL compendium enhancements. Nucleic Acids Research, 30:1, 260-263.

 

  1. Brenner SE, Koehl P, and Levitt M. (2000) The ASTRAL compendium for sequence and structure analysis. Nucleic Acids Research 28:1, 254-256.