**BALSA Pairwise Sequence
Alignment User Manual**

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

**NOTE:** All
sequences must be in FASTA format.

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.

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.

.

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.

- 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.

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

- 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.

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