Attacca

Attacca is an automatic annotator for bacterial DNA. It annotates known features (specified in a feature database) and structures specified in grammar rules.

Note

The Repository of Antibiotic-resistance Cassettes (RAC) is a web version of Attacca that you can use on our system and available for free for non-commercial users.

Example Annotations

Download

Attacca Version 0.27

StructureDisco Version 0.01

License

Attacca and StructureDisco are available for free for non-commercial use. Neither source code nor binaries can be redistributed without explicit written permission from the copyright holders.

System Requirements

Attacca uses GNU make to compile the source code. To build the application you will also need:
  1. GCC version ≥ 4.2 with C++ (i.e. g++)
  2. Xerces-C version ≥ 2.7 and < 3.0
  3. MySQL C library headers version ≥ 5.0 and < 5.1
  4. Operating system with POSIX compliant threads (e.g. Linux)
To run Attacca you will need:
  1. To configure attacca.conf for your system settings
  2. MySQL server running with a feature database according to the schema below
  3. Xerces-C and MySQL C library
  4. BLASTALL version ≥ 2.2

StructureDisco uses Apache Ant to compile the source code. To build the application you will also need:

  1. To configure experimenter.properties
  2. Java Compiler ≥ 1.5
  3. A working Attacca application
Attacca's annotation of 300 GenBank sequences and the annotations of the same sequences by three expert annotators is available in Excel (XLS) format.
You are encouraged to contact Guy Tsafnat for help with any of the above items.