##
## Configuration file for BEAP5
##
## BEAP: Blast Extension & Assembly Program
##
## FORMAT: <name> = <value>
##
##  All configuration parameters are defined with a "name" and "value"
##  connected with a '=' sign.  All names are predefined thus should not
##  be changed (if you don't want to confuse the program).  The "value"
##  syntax are described for each parameter below.  It is a strongly
##  recommended practice that all "value" strings should contain only
##  alpha-numeric characters, no spaces.
##
## COMMENT:
##
##  All lines starting with '#' symbol are "comment" lines. "Comment out"
##  refers to adding a '#' in the begining of the line to make it appear as
##  "comments" (to "disable" this line).
##
#########################################################################

##
# Absolute PATH to NCBI Blast binaries (verion 2.2.23 required) on your
# copmuter (where blastcl3, blastall, megablast, etc are located).
#-------------
myblastloc = /absolute/path/to/ncbi/blast/bin

##
# Absolute PATH to "cap3" location on your copmuter
#-------------
mycap3loc = /absolute/path/to/cap3

## 
# Input file: Plain ascii file containing DNA sequences in fasta format
#             to serve as starters (primers).
#-------------
starterseq = infile.fasta

##
# Output file: Define a customized file name 'root' (all output files will
#              be named after this root name.
#--------------
outputroot = testone

##
# Blast engine: - netblast, which uses NCBI sequence databases remotely.
#               - megablast, which uses local sequence databases.
#-------------
  blastengine = netblast
# blastengine = megablast

##
# "netblast" databases: Separate them with comma if multiple sequence db is used.
#            This option is in effect only when 'blastengine' is set to 'netblast'.
#            Find the target database names from the 'netblast' README:
#            ftp://ftp.ncbi.nlm.nih.gov/blast/documents/netblast.html ; e.g.:
#            - nr
#            - est
#            - est -u bos_taurus
#            - est_human
#            - est_others
#            - bta_genome/bta_bes 
#            - Trace/Bos_taurus_EST 
#            - Trace/Bos_taurus_OTHER
#            - Trace/bos_taurus_WGS
#            - htgs -u bos_taurus
#   For more options, see http://www.animalgenome.org/blast/doc/netblast.html
#         :: Appendix. Currently supported databases 
#         ::           A. General Nucleotide Sequence Databases
#-------------
netblastdb = nr,est -u bos_taurus,bta_genome/bta_bes,Trace/Bos_taurus_EST,htgs -u bos_taurus

##
# "megablast" databases: Separate them with comma if multiple sequence db is used.
#            This option is in effect only when 'blastengine' is set to 'megablast'.
#            The name of database to use largely depends on what you install
#            locally.  On the NAGRP server, we have:
#             - BTGI
#             - Bt.seq.uniq
#             - bov.genome.chr
#             - est_human
#             - est_mouse
#             - fasta.sus_scrofa
#             - Gga.seq.uniq
#             - GGGI
#             - Ssc.seq.uniq
#             - SSGI
#             - wgs
#   For more options, see http://www.animalgenome.org/blast/docs/blast_databases.html
#-------------
megablastdb = Bt.seq.uniq,BTGI,est_human

##
# Blast threshold: E-values (default: 1e-10)
#                  Examples: 5e-30, 3e-60, etc. 
#-------------
evalue = 2e-10 

##
# Blast threshold: Word size (default: 20)
#                  Examples: 10, 20, 30, 50, 100, etc, etc.
#-------------
words = 20

##
# Number of BEAP rounds: (default: 10; range: 5-15)
#  This is the number of times BEAP repeats blasts based on results from
#  the previous run.  Usuallly 5-10 times will achieve what you need.
#-------------
roundlimit = 10

# END
######