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README
nextorf.py
test.fas
testrp.fas
xbb_blast.py
xbb_blastbg.py
xbb_help.py
xbb_search.py
xbb_sequence.py
xbb_translations.py
xbb_utils.py
xbb_widget.py
xbbtools.py

README

Tue Aug  8 23:23:15 2000

Xbbtools
========

Xbbtools is a Graphical Sequence Editor originally written in Tcl/Tk with
BioWish. This is the start of a pure python re-implementation of xbbtools with
biopython.
Usage: xbbtools test.fas

Whats available:
      * open FASTA file
      * display 1 or 6 frame translations ala DNA Strider
      * all operations work on selection or complete sequence
      * displays start, stop, length and composition of selection
      * complement and reverse operations
      * change genetic code 
      * very simple blast run menus

TODO:
      * I'm waiting for a biopython modules for
	    - reading and writing different sequence formats
	    - spawning external programs/searches e.g. blast
	      without freezing the whole Tk mainloop
      * implement biowish's ORF Displayer
      * add Pyphy's database grabber tool
      * speedup DNA seq operations suitable for complete genomes
      * add windows support (shudder)


nextorf.py
==========
nextorf.py is a python re-implementation of the Tcl script nextorf.tcl
used together with xbbtools for ORF-fishing during the Complete Genome
Sequencing Project of the Typhus Bacteria Rickettsia Prowazekii developed
by Thomas Sicheritz-Ponten, Jan Andersson an Morten Andersen

Usage: nextorf.py testrp.fas
    or nextorf.py -h

Feel free to suggest, fix and hack
 ... have fun 
         -thomas

Sicheritz Ponten Thomas E.  CBS, Department of Biotechnology
blippblopp@linux.nu         The Technical University of Denmark
CBS:  +45 45 252485         Building 208, DK-2800 Lyngby
Fax   +45 45 931585         http://www.cbs.dtu.dk/thomas/index.html

	De Chelonian Mobile ... The Turtle Moves ...



Sicheritz-Ponten T.: BioWish: a molecular biology command extension to Tcl/Tk.
Comput Appl Biosci. 1997 Dec;13(6):621-2. 
PMID: 9475992; UI: 98136469

Andersson SG, Zomorodipour A, Andersson JO, Sicheritz-Ponten T,
Alsmark UC, Podowski RM, Naslund AK, Eriksson AS, Winkler HH,
Kurland CG: The genome sequence of Rickettsia prowazekii and the origin of mitochondria.
Nature. 1998 Nov 12;396(6707):133-40.
PMID: 9823893; UI: 99039499

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