Table of Contents

1. Using the Online Tool
1. Single Word or Multi Word
2. Alignment Parameters
3. Version
4. Advanced Options
2. Using the Generated Code
1. Compilation
2. Usage

Using the Online Tool

Single Word or Multi Word

By selecting the "Single Word" or "Multiple Word" radio buttons, you can generate code that will use single computer word bit-vectors or multiple computer word bit-vectors. Single word code will only be able to align strings where one of the strings to be aligned is less than 64 characters long. Multiple word code doesn't have this limitation, but requires more operations and thus has longer run-times, even when sequences are short.

Parameters

These are the typical similarity scoring alignment parameters of Match, Mismatch, and Gap Penalty.

Version

BitPAl comes in two "flavors", Original and Packed. The difference between the two is detailed in (..). Briefly, the two versions of BitPAl use different bit-vector representations. In general, the Packed version will offer better performance. However, for very small (in magnitude) parameter values, the Original version will have better performance.

Advanced Options

Debug Level

The BitPAl code generator has three levels of debug information.

1. Off means that no debugging information is generated.
2. Some means that debugging code is generated by the Python code in BitPAl's C output code .
3. All means that the debugging code generated by Some is generated, as well as debug printouts that are generated in the Python code

Semi Global Alignment

A semi-global alignment is an alignment where gaps are allowed without penalty at the beginning or end of the sequences to be aligned. The semi global alignment options currently implemented are:

• Allow gaps in beginning of first string
• Allow gaps in the end of the first string

To enable or disable one of the semi-global alignment options simply click On or Off.

Using the Generated Code

The code file generated by BitPAl is C that can be either compiled into an example executable or integrated into other programs.

Compilation

GCC on GNU/Linux is the compiler that was used during development, and is the recommended compiler. MinGW can be used on Windows. To compile using gcc:

gcc -o bitpal code.c

Usage

A file of generated sequence data is available to test the compiled program. To run BitPAl, compiled as above:

bitpal seqs.txt