NWGAP

NWGAP uses a modified version of the Needleman and Wunsch algorithm. The most significant modification is that affine gap penalties can be used. Other modifications include user-defined reduced "set" alphabets. A variety of alignment methods can be selected, including match/mismatch, dayhoff pam-250, structure genetics, properties, and user-defined methods.

NWGAP can be used to produce global alignments between two nucleic acid sequences, or two protein sequences.

NWGAP uses the linear space version of the dynamic programming algorithm of Miller and Myers.

Installed on the Opteron Cluster.

Opteron version

NWGAP users will find it convenient to use the /biomed/lib/examples/.login.fixed login file. It adds to your default path directories where many sequence analysis packages are stored, sets up the environment for EMBOSS, and defines some environment variables for sequence analysis packages.

• Version 2.4
• Usage:

  srun /biomed/bin/nwgap

• Example job

Other NWGAP documentation:

• User Manual for NWGAP.

See also:

• Other nucleic acid and protein sequence analysis packages installed at the PSC.