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3. Examples in this presentation from windows and unix installations.
Easy installation
Examples in this presentation from windows and unix installations.
<programe name>
Options or Auto mode
In windows a self extracting file, after installation a shortcut is created:
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4. Sequence input as database:sequence_name
Input sequence source
Local file
Local Database
web
Sequence input as database:sequence_name
showdb command: displays local databases
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5. emboss.ini
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18. Flav_azoch: Azotobacter chroococcum mcd 1 FLAVODOXIN 2
FLAVODOXIN B
Flav_azoch: Azotobacter chroococcum mcd 1
FLAVODOXIN 2
Flav_azovi: Azotobacter vinelandii
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21. Flav_soltu: Solanum tuberosum (Potato) FLAVODOXIN
FLAVONOL SYNTHASE
Flav_soltu: Solanum tuberosum (Potato)
FLAVODOXIN
Flav_rhoca: Rhodopseudomonas capsulata
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46. Others geecee fuzzpro garnier plotorf Restrict Helixturnhelix
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48.
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49. EMBOSS interfaces http://emboss.sourceforge.net/interfaces/
Command line: Windows, Cygwin
Java:
Jemboss (needs java web start)
PERL and other scripts:
Bio::Emboss Module
BioPerl EMBOSS only a part
BioPython EMBOSS only a part
Web:
EMBOSSGUI (needs Apache or other webserver)
Pise
W2H
wEMBOSS
Other GUIs:
Staden
Kaptain (KDE2)
An interface is something that comes between you and the raw horror of any computer's operating system
In EMBOSS, interfaces try to help you by making access to the programs, their options and their input and output files easier.
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51.
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52.
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53. EMBOSS suggested reading
Chapter 12 of “Sequence analysis in a nutshell” (Markel & Léon)
EMBOSS quick guide
“doc” directory for more details
Manual
Programs
Tutorials
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55. EMBOSS for UNIX Login as root
Download EMBOSS (ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS tar.gz)
gzip –d EMBOSS tar.gz
tar xvf EMBOSS tar
cd EMBOSS-6.1.0
./configure
make
make install
ENVIRONMENT SETTINGS: (can be included in .bashrc file)
PATH=$PATH:/home/workshop/EMBOSS-6.1.0/emboss
export PLPLOT_LIB=/home/workshop/EMBOSS-6.1.0/plplot/lib
export EMBOSS_DATA=/home/workshop/EMBOSS-6.1.0/emboss/data
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56. EMBOSSwin (Not in windows 98!)
Download embosswin-0.8-setup.exe from the course web page
Follow the instructions
After finishing the setup
Click EMBOSSwin shortcut (Desktop)
Proceed with examples
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57. optional variables -sbegin sequence begin position
-send sequence end position
-sreverse reverse complement the sequence
-slower change sequence to lower case
-supper change sequence to upper case
-osformat output sequence format
-help show help
-options ask for optional parameters
-auto run silently (for use in scripts, e.g. perl)
-sask prompt user for start & end of input sequence
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58. Making own customized DBs
Retrieve sequences of interests or whole dbs
dbiflat -idformat swiss -dbname dgdb.dat -directory . -release 1.0 -date 05/10/12 -fields AC -verbose
Modify emboss.ini in windows or .embossrc file in unix to include information about the new db
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