IGEM:Harvard/2006/Container Design 5: Difference between revisions
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== Oligo list == | |||
[[Media:oligo_list.txt|oligo sequence list]]<br> | |||
==oligo path== | ==oligo path== |
Revision as of 12:11, 24 July 2006
Oligo list
oligo path
Schematics and .AI Files
-
Double-Ply Barrel Schematic
(ai file) -
Double-Ply Lid 2D Schematic, Plus "Up" & "Down" Points
(ai file) -
Double-Ply Barrel and Lid In-Out Schematic
(ai file) -
Double-Ply Barrel 2D Schematic, Plus "In" & "Out" Points & Latch Points
(ai file)
Automated schematic
Here's a link to a python file that automatically creates a schematic. Call maked(inf,outf) where inf is a token list and outf is the file you'd like to output to (should be .bmp). It uses a nifty module called pygame. I haven't tried it out on Macs yet. Still, it gives fairly colorful results.
-
Design 5 barrel
ASCII Diagrams
- Double-Ply Barrel (42-helix outer barrel)
... ... 070 068 066 064 ... ... ... 071 069 067 065 063 ... ... 030 000 002 004 062 ... ... 031 029 001 003 005 061 ... ... 032 028 ... ... 006 060 ... 033 027 ... ... ... 007 059 034 026 ... ... ... 008 058 035 025 ... ... ... ... 009 057 036 024 ... ... ... ... 010 056 037 023 ... ... ... 011 055 038 022 ... ... ... 012 054 ... 039 021 ... ... 013 053 ... ... 040 020 018 016 014 052 ... ... 041 019 017 015 051 ... ... 042 044 046 048 050 ... ... ... 043 045 047 049 ... ...
- Double-Ply Lid (19 helices long)
... 000 002 004 006 008 010 012 014 016 ... 037 001 003 005 007 009 011 013 015 017 ... 036 034 032 030 028 026 024 022 020 018 ... ... 035 033 031 029 027 025 023 021 019 ...
scaffold splitting
Barrel
!/usr/bin/python import string import sys import fileinput def nowhite(s): return ''.join([c for c in s if c in string.letters]) seq = '' # read in sequence for line in fileinput.input("-"): seq = seq + nowhite(line) box_1 = 96 * 32 + 72 loop = 66 box_2 = 11 + 12 + 96 * 6 + 68 box_3 = 16 + 12 + 6 * 96 + 65 box_4 = 19 + 12 + 6 * 96 + 65 box_5 = 19 + 12 + 6 * 96 + 68 box_6 = 16 + 12 + 6 * 96 + 72 box_7 = 12 + 12 + 3 * 96 box_1_seq = seq[:box_1] seq = seq[box_1:] loop_1_seq = seq[:loop] seq = seq[loop:] box_2_seq = seq[:box_2] seq = seq[box_2:] loop_2_seq = seq[:loop] seq = seq[loop:] box_3_seq = seq[:box_3] seq = seq[box_3:] loop_3_seq = seq[:loop] seq = seq[loop:] box_4_seq = seq[:box_4] seq = seq[box_4:] loop_4_seq = seq[:loop] seq = seq[loop:] box_5_seq = seq[:box_5] seq = seq[box_5:] loop_5_seq = seq[:loop] seq = seq[loop:] box_6_seq = seq[:box_6] seq = seq[box_6:] loop_6_seq = seq[:loop] seq = seq[loop:] box_7_seq = seq[:box_7] seq = seq[box_7:] extra_scaffold = seq barrel = box_1_seq + box_2_seq + box_3_seq + box_4_seq + box_5_seq + box_6_seq + box_7_seq #print out the length of each segment and its sequence barrel_file = file('barrel_scaffold.txt', 'w') print len(barrel) print barrel barrel_file.write(barrel)
Lids
#!/usr/bin/python import string import sys import fileinput def nowhite(s): return ''.join([c for c in s if c in string.letters]) seq = '' # read in sequence for line in fileinput.input("-"): seq = seq + nowhite(line) scaffold_len = 7572 lid_1 = 96 * 38 lid_2 = 96 * 38 linker_len = scaffold_len - lid_1 - lid_2 linker_1 = linker_len / 2 #store first segment up to end of lid 1 lid_1_seq = seq[:lid_1] #reset sequence to start at end of lid 1 seq = seq[lid_1:] linker_1_seq = seq[:linker_1] seq = seq[linker_1:] lid_2_seq = seq[:lid_2] seq = seq[lid_2:] #linker 2 is the rest of the scaffold linker_2_seq = seq # check to make sure linker 1 and linker 2 are the same length if(len(linker_1_seq) != len(linker_2_seq)): print 'Error: linker 1 is not the same length as linker 2' #print out the length of each segment and its sequence lid_1_file = file('lid_1_scaffold.txt', 'w') lid_2_file = file('lid_2_scaffold.txt', 'w') print len(lid_1_seq) print lid_1_seq lid_1_file.write(lid_1_seq) print len(linker_1_seq) print linker_1_seq print len(lid_2_seq) print lid_2_seq lid_2_file.write(lid_2_seq) print len(linker_2_seq) print linker_2_seq