Installing Sequery

1. Introduction
2. Getting and Installing Sequery
• Troubleshooting Shell Scripts
3. Other Scripts and Tools Provided with Sequery
4. Algorithmic Details of Sequery
5. Contact Information

Introduction

Sequery is a tool to search the sequences of the protein structures in the Protein Data Bank (PDB) for a particular pattern of residues, which may include exact matches and acceptable substitutions based on a user-specified amino acid substitution matrix and/or a numerical threshold. Sequery was developed by Michael E. Pique, Michael A. Siani, Leslie A. Kuhn, Elizabeth D. Getzoff, and John A. Tainer, Department of Molecular Biology, The Scripps Research Institute and is distributed here with permission of the authors. Development of Sequery was supported in part by NSF grant BIR9631436.

A useful complement to Sequery is SSA (Superpositional Structure Assignment), which automates the assignment of secondary structure to tetrapeptides identified by a Sequery search. For more information and software availability, see SSA Information and Documentation.

For literature references related to Sequery, please see the section on Algorithmic Details.

Usage information for Sequery can be found in Using Sequery

Back to Table of Contents

Getting and Installing Sequery

Sequery will work on any UNIX system with a C-compiler and has been tested on Sun hardware running Solaris and SGI hardware running Irix. Additional scripts require awk, C-shell (csh) and Bourne-shells (sh) installed, as well as an accessible copy of the Protein Data Bank.

The latest version of Sequery, as well as the most recent version of this documentation, can be found at the home page for the Protein Structural Analysis and Design Laboratory, Department of Biochemistry, Michigan State University, and is distributed here with permission of the co-authors at The Scripps Research Institute, Michael Pique, Elizabeth Getzoff, and John Tainer. To install Sequery, perform the following steps:

• Download sequery.tar.Z
• Place this file in the directory into which you wish to install the software, and enter the following command:

zcat sequery.tar.Z | tar xvf -

• To compile the software, type the following command from the directory in which Sequery was unpacked:
• make install
  (Note: This defaults to using the current directory as the root directory for Sequery. If this is not desired, alter the makefile to include the desired location where noted in the makefile. Also, if Sequery is later moved from this location, it will need to be recompiled to work correctly.)
• There are a few additional modifications that must be made in some of the scripts in sequery/share to point to the correct file and directory locations. These locations will be specific to your system. All settings are at the top of the script code. The scripts and variable settings needed are as follows:

  Script Name	Variable to Set at the top of the script
  addname	PDBHOME
  genpdbselectseq	PDBHOME SEQUERY_HOME
  minipdbextract	PDBHOME

  The PDBHOME variable should be set to the directory of the Protein Data Bank files (e.g. /usr/pdb)
  The SEQUERY_HOME variable should be set to the directory in which Sequery was installed (e.g. /usr/bin/sequery)

Back to Table of Contents

Troubleshooting Shell Scripts

Located in the Sequery/share directory are several shell scripts, all of which assume the C-shell and Bourne-shell are installed in the standard locations, which are /bin/csh and /bin/sh. If you have difficulty running one or more of these scripts, you may edit the first line of each script to point to the correct shell location for your system. Sequery scripts which are dependent on shell locations include:

Additionally, these scripts assume you have awk, nawk, or gawk (different implementations of a simple column- or field-oriented programming language) running on your system. (See The Free Software Foundation (GNU) web site for more information on obtaining and using gawk.)

Back to Table of Contents

Other Scripts and Tools Provided with Sequery

• addname -- adds protein name from the PDB file to end of Sequery output line. Output to stdout. This is useful for noting functional patterns in the proteins that match.

• genpdbselectseq -- generates a sequence file which contains the amino acid sequences along with PDB codes, and chain IDs and which is used by Sequery to search for pattern matches, for each of the PDB files in the PDB Select list.

• genpdbseq -- generates a sequence file as a Sequery search database from a PDB file or series of PDB files. Output is directed to stdout.

• minipdbextract -- generates a PDB formatted file for the residues in each line of Sequery output. It takes the start residue, end residue, and pdbcode from Sequery output, searches the $PDBHOME database for that protein, and extracts coordinate lines from the PDB files.

Back to Table of Contents

Algorithmic Details of Sequery

Sequery was developed as a successor to Searchwild, which is described in

Collawn JF, Kuhn LA, Liu LF, Tainer JA, Trowbridge IS
Transplanted LDL and mannose-6-phosphate receptor internalization signals promote high-efficiency endocytosis of the transferrin receptor
EMBO J., 10(11) (Nov): 3247-3253 (1991)

Collawn JF, Stangel M, Kuhn LA, Esekogwu V, Jing SQ, Trowbridge IS, Tainer JA
Transferrin receptor internalization sequence YXRF implicates a tight turn as the structural recognition motif for endocytosis
Cell, 63(5) (Nov 30): 1061-1072 (1990)

Other references related to the use of Sequery include the following:

Craig L, Sanschagrin PC, Rozek A, Lackie S, Kuhn LA, Scott JK
The Role of Structure in Antibody Cross-Reactivity Between Peptides and Folded Proteins
J. Mol. Biol., 281(1) (Aug 7): 183-201 (1998)

Chang CP, Lazar CS, Walsh BJ, Komuro M, Collawn JF, Kuhn LA, Tainer JA, Trowbridge IS, Farquhar MG, Rosenfeld MG
Ligand-induced internalization of the epidermal growth factor receptor is mediated by multiple endocytic codes analogous to the tyrosine motif found in constitutively internalized receptors
J. Biol. Chem., 268(26) (Sep 15): 19312-19320 (1993)

Back to Table of Contents

Contact Information

Questions should be directed to Dr. Leslie Kuhn at:

or to Michael Pique at: