ApE

ApE (A Plasmid Editor) is a freely available DNA Manipulation and visualization program. I works on macOS and Windows as well as on Linux.

It is not necessary to install ApE to use it, you can use it from a folder on your desktop.

Go here to get ApE, click on the link for your OS as indicated below.

Introduction to ApE

How to linearize a circular sequence at a specific location.

1. Locate the cursor at the desired location where you want to cut the vector. Make sure sequence is circular.

1. Select ApE Edit>“Linearize @ insert site” (see below).

The sequence is now linear beginning at the location of the cursor.

More info

https://github.com/gear-genomics/wily-dna-editor

Annotate the PTC sequence with ApE

https://wiki.tcl-lang.org/page/sha1

def SmallestRotation(s):
"""Find the rotation of s that is smallest in lexicographic order.
Algorithm according to Duval 1983:
Pierre Duval, Jean. 1983. “Factorizing Words over an Ordered Alphabet.”
Journal of Algorithms & Computational Technology* 4 (4) (December 1):
363–381.
Algorithms on strings and sequences based on Lyndon words.
David Eppstein, October 2011.
https://gist.github.com/dvberkel/1950267
"""
prev, rep = None, 0
ds = 2 * s
lens = len(s)
lends = len(ds)
old = 0
k = 0
w = ""
while k < lends:
i, j = k, k + 1
while j < lends and ds[i] <= ds[j]:
i = (ds[i] == ds[j]) and i + 1 or k
j += 1
while k < i + 1:
k += j - i
prev = w
w = ds[old:k]
old = k
if w == prev:
rep += 1
else:
prev, rep = w, 1
if len(w) * rep == lens:
return w * rep

https://openwetware.org/wiki/Software

changed here!

append result “[format “LOCUS %-16s %+11s bp %-3s%-6s %-8s %-3s %-11s” $genban{k}_{l}ocu{s}_{n}ame[stringlength$text] $stranded$genbank_type $info($w,circular) $genbank_division_code [string toupper [clock format [clock seconds] -format “%d-%h-%Y”]]]\n”

append result “[format “LOCUS %-16s %+11s bp %-3s%-6s %-8s %-3s %-11s” $genban{k}_{l}ocu{s}_{n}ame[stringlength$text] $stranded$genbank_type $info($w,circular) $genbank_division_code [string toupper [clock format [clock seconds] -format “%d-%h-%Y”]]]\n”

Also
6. ABI files can be linked into sequence files by dragging the link icon from
the ABI window onto a sequence window. When the sequence window is saved, the
data from the abi file is saved with it in a text-encoded format so that the
file can still be opened with a text editor.

space in filename

parse $argv into filenames even if these are spaces
or
tell gnome-open that every filename should be enclosed by ""

a
aaa
c
ccc

cut paste

line 3857
AppMain.tcl

http://tech.groups.yahoo.com/group/wikidPad/message/4527
<<
PRIMARY selection doesn’t exist or form “STRING” not defined
PRIMARY selection doesn’t exist or form “STRING” not defined gggatcc
while executing
“selection get -displayof $w-selectionPRIMARY"(procedure"cli{p}_{p}aste"line7)invokedfromwithin"cli{p}_{p}aste$w”
(procedure “keyevent_manager” line 113)
invoked from within
“keyevent_manager .dna_window1 Control v ”
(command bound to event)

Sunday, June 07 2009

paste function

proc clip_paste {w {direction normal}} {
global info
global tcl_platform

tk_messageBox -message “clip paste”

if {($tcl_platform(platform) == “unix”) && ([tk windowingsystem] != “aqua”)} {

sputs paste:CLIPBOARD:[selection get -displayof $w -selection CLIPBOARD]

sputs paste:PRIMARY:[selection get -displayof $w -selection PRIMARY]

if {[catch {set text [selection get -displayof $w -selection PRIMARY]}] != 0} {return}

# }  ###
# else  ###
# {                                                                                       ###
if {[catch { set text [selection get -displayof $w -selection CLIPBOARD]}] != 0} {return}

}