IGEM:Harvard/2006/Container Design 4: Difference between revisions
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===Scaffolds (KV, 6.29.06)=== | ===Scaffolds (KV, 6.29.06)=== | ||
[[Image:barrel_scaffold.gif|thumb|schematic of 30hb barrel]] | |||
[[Image:lid_1_schematic.gif|thumb|schematic of lid 1]] |
Revision as of 11:35, 29 June 2006
Design details
based on n = 0.324 nm, d = 3.0 nm
Shape | Lid ply | Cylinder design | Lid design | Total scaffold length |
honeycomb hexagon | single | 30 tubes (29.0 nm dia) x (84+12)bp long (30.8 nm) = 2880bp | 13 tubes (34.2 nm) x (84+12)bp long (30.8 nm) = 1248bp each | 2880+(2*1248) + 6bp + 12bp linkers = 5394 |
ASCII Files
Lid 1:
000 002 004 006 008 010 012 ... 001 003 005 007 009 011 ...
Barrel:
... ... 000 002 004 ... ... 029 001 003 005 ... ... 028 ... ... 006 ... ... 027 ... ... ... 007 ... 026 ... ... ... 008 025 ... ... ... ... 009 024 ... ... ... ... 010 ... 023 ... ... ... 011 ... 022 ... ... ... 012 ... 021 ... ... 013 ... ... 020 018 016 014 ... ... ... 019 017 015 ...
Lid 2:
000 002 004 006 008 010 012 ... 001 003 005 007 009 011 013
Sequence Chunks (KV, 6.27.06)
Script for generating sequence chunks
#!/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) lid_1 = 96 * 13 linker_1 = 30 box = 29 * 96 linker_2 = 30 lid_2 = 96 * 14 linker_3 = 200 box_2 = 96 #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:] box_1_seq = seq[:box] seq = seq[box:] linker_2_seq = seq[:linker_2] seq = seq[linker_2:] lid_2_seq = seq[:lid_2] seq = seq[lid_2:] linker_3_seq = seq[:linker_3] seq = seq[linker_3:] box_2_seq = seq[:box_2] seq = seq[box_2:] extra_scaffold = seq barrel = box_1_seq + box_2_seq #print out the length of each segment and its sequence print len(lid_1_seq) print lid_1_seq print len(linker_1_seq) print linker_1_seq print len(barrel) print barrel print len(linker_2_seq) print linker_2_seq print len(lid_2_seq) print lid_2_seq print len(linker_3_seq) print linker_3_seq
Modifications to William's program to print each oligo number next to what tokens it represents
oligo_num = 0 for oligo in OTP_ra: for token in oligo: print str(oligo_num) + ": ", token oligo_num = oligo_num + 1
Modifications to William's program to print a grid of oligo numbers completely filled in
- add this part to main (AAA or BBB)
#### # generate and print the oligo grid #### # Initialize the grid with all periods num_strands = len(TPP_ra) num_subzones = len(TPP_ra[0]) sub_token_visit_ra = ['.' for subzone_num in range(num_subzones)] grid_ra = [sub_token_visit_ra[:] for strand_num in range(num_strands)] oligo_num = 0 for oligo in OTP_ra: grid_ra = generate_oligo_path(oligo, oligo_num, grid_ra) oligo_num = oligo_num + 1 print grid_ra print_all_oligos(grid_ra, num_strands, num_subzones)
- add this part to honeycomb_pointers_v1.py
# The idea here is to have a function that adds the numbers of one oligo path # to the appropriate places in the big grid array. Eventually this will be printed # in main. Also it needs to be initialized in main. Oligo_path is the path of # one oligo, while grid_ra is the grid that is constantly being updated until # it is printed in main. oligo_num is number that will be inputed to the grid_ra. def generate_oligo_path(oligo_path, oligo_num, grid_ra): num_path_tokens = len(oligo_path) # Assign visits for path_token_num in range(num_path_tokens): token = oligo_path[path_token_num] strand = token[0] subzone = token[1] grid_ra[strand][subzone] = oligo_num return grid_ra def print_all_oligos(grid_ra, num_strands, num_subzones): spacer = ' ' for strand_num in range(num_strands): for subzone_num in range(num_subzones): visitor_string = str(grid_ra[strand_num][subzone_num]) sys.stdout.write(visitor_string) sys.stdout.write(spacer[:4 - len(visitor_string)]) sys.stdout.write('\n')
honeycomb_pointers_v1.py UPDATED
BBB_make_honeycomb_structure_v1.py UPDATED
Sequence Chunks (TChan, 6.27.06)
- Media:Chunk1p7308_TC_62706.txt
- Chunk of p7308 sequence for container4's lid1.
- Media:Chunk2p7308_TC_62706.txt
- Chunk of p8256 sequence for container4's barrel (skips 6bp after lid1's chunk, 6bp right before lid2, the 96bp*13helices that is lid2, 6bp after lid2, and appends the final helix).
- Media:Chunk3p7308_TC_62706.txt
- Chunk of p7308 sequence for container4's lid2.
Oligos (TChan, 6.27.06)
- Media:lid1_7308_TC_62706.txt
- Oligos for lid 1 (correct wordcount: 30lines, 30words, 1122chars (includes 30 carriage returns) for (96bp-12ssbp)*13helices)
- Media:barrel_7308_TC_62706.txt
- Oligos for barrel (correct wordcount: 74lines, 74words, 2594chars (includes 74 carriage returns) for (96bp-12ssbp)*30helices)
- Media:lid2_7308_TC_62706.txt
- Oligos for lid 2 (correct wordcount: 30lines, 30words, 1122chars (includes 30 carriage returns) for (96bp-12ssbp)*13helices)