General information about needle tools

BMERC : needle tools : Introduction : General information

Table of contents

  1. General information about needle tools
    1. Table of contents
    2. What is needle tools?
    3. Credits and acknowledgements
    4. Documentation conventions
    5. Using needle tools

What is needle tools?

First off, what is needle?

The needle program solves the general pairwise protein threading problem: Given a core (a model of a protein structure), a protein sequence, and a function that assigns a score to a given alignment of sequence to structure, needle finds the optimum alignment of the sequence to the core. The score function may include singleton, pairwise, and sequence-composition-dependent loop terms, and may be specified in several ways, usually by a set of score and environment files. needle is an application of the Branch and Bound algorithm to protein threading, and is written in Common Lisp.

OK, what are "needle tools" then?

The needle tools suite constructs the cores and their associated score files used by needle. Other programs that are useful for manipulating proteins as structures or sequences are also included. needle tools is implemented as a collection of small programs written mostly in perl and C for use with the Unix operating system, and held together using make.

How do I get needle tools?

For instructions on how to obtain and install this software, please refer to the needle tools installation page.

Credits and acknowledgements

Many people have worked on this tool suite over the years. Ljubomir Buturovic, Raman Nambudripad, and Temple Smith developed the original MRF software and defined most of the file formats . . . [finish. -- rgr, 21-Feb-97.]

[credit to Eisenberg lab for exposure code. -- rgr, 21-Feb-97.]

And finally, Bob Rogers <rogers@darwin.bu.edu> is responsible for mangling it into its present form.

Documentation conventions

[probably want to expand this. -- rgr, 5-Mar-97.]

In the "Known Bugs" sections for each tool, those bugs that affect the current release are marked with "***", with dated notes identifying when the bug was repaired at BMERC (but the stars stay until the next release, even though the code may work at BMERC). Descriptions of older bugs are kept for reference purposes; it is sometimes important to know whether a certain bug was still at large when a given file was created.

Using needle tools

Note: It is not sufficient to run these programs by specifying them by their full pathname, since some require undocumented internal scripts, perl libraries, or programs that must be found via the Unix PATH mechanism.

In csh, you must update your PATH environment variable by doing the following: 

    source ~thread/bin/scripts/init-needle-tools
(though the full pathname is only correct at BMERC). init-needle-tools is smart about maintaining multiple binary directories for different system types. Because it is "sourced" and not invoked as an ordinary script, there are no arguments, and it is also necessary to use the full pathname of the file. At BMERC, this is ~thread/bin/scripts/init-needle-tools.

Note: The programs ending in .pl are scripts written in the "perl" programming language. perl is easy to modify, but hard to read, and can be harder still to debug. Bear that in mind if you want to customize any of these scripts.


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Bob Rogers <rogers@darwin.bu.edu>
Last modified: Fri Nov 26 19:56:57 EST 1999