[ Program Manual | User's Guide | Data Files | Databases ]
Names identifies GCG data files and sequence entries by name. It can show you what set of sequences is implied by any sequence specification.
The expression % names *bov* displays every GCG data file or sequence entry whose name contains the pattern bov. The purpose of the Names program is to show what entries and filenames correspond to a GCG sequence specification. Sequence specification is described in detail in Chapter 2, Using Sequence Files and Databases of the User's Guide.
Names asks you what you want to call the output file. If you press <Return> in answer to this query, Names shows the names on your terminal screen in a format similar to a directory listing. Otherwise, Names writes a list file containing the names of all of the entries corresponding to your sequence specification. The list file is suitable for input to any Wisconsin Package(TM) program that supports indirect file specification.
If you run Names with the command-line parameter -SHOwfiles, it documents the list file. For each sequence entry or file in the list file, Names adds as much of the entry's documentation as will fit between the end of the entry's name and column 132. Sequence entries and filenames are easier to identify when the list file is printed on a 132-column printer or terminal screen. The documented output file is still suitable for input to any Wisconsin Package program that supports indirect file specification. You can set the column where the documentation is cut off to any number between 20 and 511.
If your sequence specification contains no logical name or directory specification, Names looks in all the databases and in all the GCG data directories to find all possible entry names. The expression % names hum* would do almost the same thing as the command % names GenBank:hum*, except that if any sequences beginning with hum were present in databases other than GenBank or in any GCG data directories, they would also be identified.
Keep in mind that filenames are case sensitive and database entry names are case insensitive. Because this program searches for both filenames and database entry names, you must take care when you enter the character pattern that makes up your specification.
For example, if you entered Gamma* as a file specification, this program would find all entries in the databases whose names begin with Gamma but no GCG-supplied files would be found. This is because all the files in the Wisconsin Package are named using lowercase letters. Conversely, if you entered gamma*, this program would find all of the entries in the databases and all the GCG-supplied files whose names begin with gamma.
Here is a session using Names to make a documented list file for most of the GenBank human beta globin sequences:
% names NAMES for what GCG data file(s) ? GenEMBL:HumHb* What (file of filenames) output file (* TERM *) ? humanbeta.fil gb_pr:humhb16aa gb_pr:humhb1az /////////////// gb_pr:humhbvintz gb_pr:humhbvxdna Names written into "humanbeta.fil". %
Here is part of the output file (the lines in humanbeta.fil contain 132 characters each; we've truncated them for this document):
!!SEQUENCE_LIST 1.0 ! NAMES from: genembl:humhb* September 26, 1996 15:59 .. gb_pr:humhb16aa LOCUS HUMHB16AA 1216 bp mRNA PRI 15-JUN-1990 DEFINITION gb_pr:humhb1az LOCUS HUMHB1AZ 483 bp DNA PRI 08-NOV-1994 DEFINITION Hum gb_pr:humhb24 LOCUS HUMHB24 2231 bp mRNA PRI 18-APR-1991 DEFINITION Hum ////////////////////// ( Some data not shown ) //////////////////////// gb_pr:humhbvint LOCUS HUMHBVINT 1342 bp DNA PRI 15-JUN-1988 DEFINITION gb_pr:humhbvintz LOCUS HUMHBVINTZ 61 bp DNA PRI 31-MAR-1995 DEFINITION gb_pr:humhbvxdna LOCUS HUMHBVXDNA 4072 bp mRNA PRI 28-FEB-1995 DEFINITI
Unknown.
The database programs Lookup, Names, StringSearch, FindPatterns, FastA, TFastA, and WordSearch can be used for list refinement if you are looking for sequences with something in common. For instance, you could identify human globin nucleotide sequences with Lookup. The output list from Lookup could then be refined further with FindPatterns to show only those human globin sequences containing EcoRI sites. You could then do a sequence search on the output from FindPatterns with FastA to see if a sequence you have is similar to any of these EcoRI-containing human globin sequences.
You can add two lists together by simply appending one of the files to the other. It is better if you use a text editor to modify the heading of the combined list so that the annotation in the list correctly reflects what you have done. Remember to delete the text heading from the second file so that it does not occur in the middle of the list.
Suppress any item in a list by typing an exclamation point (!) in front of the item. You can also put comments into a list anywhere on a line by placing an exclamation point before the comment.
All parameters for this program may be put on the command line. Use the parameter -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
Minimal Syntax: % names [-INfile=]GenEMBL:Humhb* -Default Prompted Parameters: [-OUTfile=]Term output file name (defaults to your terminal) Options: -SHOwfiles=132 limits documentation in the output file to column 132 -NOHEAding suppresses the heading at the top of the file. -NOMONitor suppresses the screen monitor
None.
The parameters listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
Names normally prints the beginning of the documentation at the top of each sequence (or file) in the list file next to the sequence's name. The value for this parameter is the column at which this documentation is cut off. -NOSHOwfiles suppresses the documentation next to each sequence name altogether.
suppresses the heading at the top of the list file that shows the input specification and the time. -HEAding is the default; disable it with -NOHEAding.
This program normally monitors its progress on your screen. However, when you use -Default to suppress all program interaction, you also suppress the monitor. You can turn it back on with this parameter. If you are running the program in batch, the monitor will appear in the log file.
[ Program Manual | User's Guide | Data Files | Databases ]
Documentation Comments: doc-comments@gcg.com
Technical Support: help@gcg.com
Copyright (c) 1982, 1983, 1985, 1986, 1987, 1989, 1991, 1994, 1995, 1996, 1997 Genetics Computer Group, Inc. a wholly owned subsidiary of Oxford Molecular Group, Inc. All rights reserved.
Licenses and Trademarks Wisconsin Package is a trademark of Genetics Computer Group, Inc. GCG and the GCG logo are registered trademarks of Genetics Computer Group, Inc.
All other product names mentioned in this documentation may be trademarks, and if so, are trademarks or registered trademarks of their respective holders and are used in this documentation for identification purposes only.