# Property file for CAD-PAM Program # # # #--------------------Sequence Modifications------------------# #Input sequence type (DNA or PROTEIN, default type is DNA) seqType=DNA #Sequence Optimization: on / off optimize=off # #provide codon file name (default=ecoli-k12) codonFile= # #remove sequences separated by ";" (functional when optimize=on) removeSequences= # #%GC adjustment (Suggested values: 0.08, 0.1, 0.12) #(Note: higher the value, lower the GC content) GCTradeOfValue= #-----------------------Oligo Design-------------------------# #Generate oligo sequences by "length" or "tm"? pickSequenceBy=length # #If by length, specify oligo length (default=40 nt). chipSeqLen=50 # #Currently set to 4 base pair long chipExtraSeqLen=0 endFillUp=yes # #Tm of oligo overlapping region (default=55C) oligoTM=55 #For Tm calculation (use default under most conditions) DNAConcentration= saltConcentration= #--------------------Oligo Chip-Synthesis--------------------# # #Production chip oligos sense5endAddOn=GTCAATAAGAGCCGCT # reference for sense3 = GCTATTCCAAGCGAC sense3endAddOn=AGTCGCTTGGAATAGC # #selection chip A oligos addon selectionA5endAddOn=GAACCGTCTCAGTGC #selection3endAddOn original GTTGGACACCGTCAT selectionA3endAddOn=ATGACGGTGTCCAAC # #selection chip B oligos addon selectionB5endAddOn=GTTAAGGCCGAAGTG #selection3endAddOn reference =CTCCATGCTCTCACC selectionB3endAddOn=GGTGAGAGCATGGAG # #Selection chip oligos fill up length selectionFillUpLen=0 # #Selection oligo TM (default=60C) selectionChipTM=60 #-------------------DNA Sequence Assembly--------------------# #Long DNA break down type #No break down:1 #Break down by RE site:2 #Break down by size:3 #Default is no break breakDownType=1 #Break down long DNA by Size #The default break down size is 400 breakSize=400 #If break down the long DNA by size, #what is the overlap size between 2 DNA fragments #The default overlap size is 40 overLapSize=40 #Break down long DNA at following type-IIS RE site sequences: #reSite=sense; antisense reSites=acctgc; gcaggt; ggtctc; gagacc # #Adding universal primers at the 2 ends of the broken fragments #yes=1, no=0 addUPrimers=0 UPrimerFileLocation=/home/ifx/cadpam062505/resources/uniquePrimerForRecoli.txt #Oligo pool size for assembly (an even number) poolSize=0 #------------------------------------------------------------#