Bigeoverlap
BIGEOVERLAP
FUNCTION
BigEOverlap compares two sets of DNA sequences to each other in both orientations using a WordSearch style comparison. EOverlap is an extended version of GCG's Overlap for use in database nonredundancy checks, together with the FilterOverlap program. BigEOverlap has a very high limit on total sequnec length for genome scale sequence analysis, but it too large for general use on most systems.
DESCRIPTION
BigEOverlap is simply a version of EGCG's EOverlap program with the sequence limit greatly increased. This makes BigEOverlap too large to run on many systems, so it is installed as a separate program.
For more information on the program, see the EGCG Program Manual entry for EOverlap.
AUTHOR
This GCG program was modified by Peter Rice (E-mail: pmr@sanger.ac.uk 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 (egcg@embnet.org).
RELATED PROGRAMS
GCG's WordSearch uses the same comparison algorithm as EOverlap. WordSearch, however, accepts a single query sequence as input and finds regions of similarity rather than overlaps. ELineUp is a screen editor for editing and displaying overlapping sequences.
RESTRICTIONS
The total length of bases in any sequence set may not exceed 3,500,000. No sequence in the query set may exceed 750,000 bases.
COMMAND-LINE SUMMARY
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.
Minimal Syntax: % bigeoverlap [-INfile1=]Mu*.Seq -Default Prompted Parameters: [-INfile2=]Mu*.Seq second search set -WORdsize=5 length of word for a match -STRIngency=.80 minimum fraction of required word matches -MINOverlap=10 minimum overlap length -INTegrate=3 number of diagonals to integrate [-OUTfile=]overlap.dat output file Local Data Files: None Optional Parameters: -UPPERlimit=.90 upper limit on stringency
LOCAL DATA FILES
None.
Printed: April 22, 1996 15:52 (1162)