Inverted looks for imperfect inverted repeats in a nucleotide sequence.
This program was originally written by Richard Durbin and Jean Thierry-Mieg as part of the ACEDB genome database package.
This version was modified for inclusion in EGCG by Peter Rice (E-mail: email@example.com Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).
All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (firstname.lastname@example.org).
Here is a sample session with Inverted
% inverted INVERTED uses nucleotide sequence data INVERTED of what sequence ? GenEMBL:hsts1 Start (* 1 *) ? End (* 18596 *) ? 1000 What gap penalty (* 12 *) ? What minimum score threshold (* 50 *) ? 35 What match score (* 3 *) ? What mismatch score (* -4 *) ? What should I call the output file (* hsts1.inv *) ? %
The output from Inverted is a simple report of hits in the sequence.
INVERTED of em_pr:hsts1 check: 1391 Score 236: 108/130 ( 83%) matches, 0 gaps . . . . . 13 GCTACGCGAGAGGCTGAGGCAGCAGAATTACTTGAACCCAGGAGGCGGAG 62 ||||| | ||||||||||||| |||||| |||||||| |||||| ||| 328 CGATGAACCCTCCGACTCCGTCTTCTTAACGAACTTGGACCCTCCGTCTC 279 . . . . . 63 GTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGTGAGAGAG 112 ||||||||||||| ||||| ||| || ||||||||||||| || |||| 278 CAACGTCACTCGGTTCTAGGCTGGTAACATGAGGTCGGACCCGCTGTCTC 229 . . . 113 CGAGACTCTGTCTCAAAAAAAAAAAAAAAA 142 | ||||| | | |||||||||||||||| 228 GTTCTGACAGGGTTTTTTTTTTTTTTTTTT 199 Score 40: 28/36 ( 77%) matches, 1 gaps . . . 853 GGCGGAGCGCGGGACGGCCGCGGGAAAAGGCGCGCGG 889 ||||| ||| ||||||| || || ||| |||||| 996 CCGCC-CGCCCCCTGCCTCCGTCCGCTTCACCGCGCC 960
The input file for Inverted is a GCG nucleotide sequence file.
All parameters for this program may be put on the command line. Use the option -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 qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.
Minimum Syntax: % inverted [-INfile=]GenEmbl:hsldlr02 -Default Prompted Parameters: -BEGin=1 -END=100 Range of interest [-OUTfile=]hsldlr02.inv Output file -THRESHold=50 Score threshold -MATCH=3 Score for a matching pair of bases -MISMATCH=-4 Score for a non-matching pair of bases -GAP=12 Score penalty for a single base gap Local Data Files: None Optional Parameters: -ORIGinal=stdout Produce original mimimal output format
The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.
requests the output format of the original inverted program, optionally with an output file name (the default is to write to the terminal).
Printed: April 22, 1996 15:53 (1162)