This is a light-weight adaptation of klib to facilitate various types of Smith-Waterman alignment, but more importantly do so interactively.

The following four alignment modes are supported:

• Local alignment: a sub-sequence of the query aligned to a sub-sequence of the target
• Glocal: the full query aligned to a sub-sequence of the target
• Extension - a prefix of the query aligned to a prefix of the target
• Global - full query aligned to the full target

The utility reads the query and target sequences from standard input, so running it without anything on standard input will cause it to never exit. The query should be on the first line, while the target on the second line. Subsequent lines should alternate between query and target.

This tool can be run interactively. Meaning, the tool reads in one query and target at a time, runs alignment, then writes the alignment output, then waits for more input. Therefore, we can wrap this tool in a process that writes to the standard input of this tool, waits for the alignment result on standard output, then does something else, then feeds more data to standard input.

Clone this repository:

git clone --recursive [email protected]:nh13/ksw.git

Note the use of --recursive. This is required in order to download all nested git submodules for external repositories.

To get version displayed in the utility, do the following:

cp post-commit .git/hooks/post-commit;
chmod +x .git/hooks/post-commit;

Finally, to compile, type:

make

The executable is named ksw.

To run tests, type:

make test

To install to /usr/local/bin, type:

make install

For a custom location (ex. ~/local/bin), type:

make install PREFIX=~/local/bin