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01/20/10 11/01/2015. Easy installation Examples in this presentation from windows and unix installations. –Options or Auto mode In windows a self extracting.

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Presentation on theme: "01/20/10 11/01/2015. Easy installation Examples in this presentation from windows and unix installations. –Options or Auto mode In windows a self extracting."— Presentation transcript:

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3 Easy installation Examples in this presentation from windows and unix installations. –Options or Auto mode In windows a self extracting file, after installation a shortcut is created:

4 01/20/10 11/01/2015 Input sequence source –Local file –Local Database –web Sequence input as database:sequence_name showdb command: displays local databases

5 01/20/10 11/01/2015 emboss.ini

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18 FLAVODOXIN B Flav_azoch: Azotobacter chroococcum mcd 1 FLAVODOXIN 2 Flav_azovi: Azotobacter vinelandii

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21 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 http://emboss.sourceforge.net/

49 01/20/10 11/01/2015 EMBOSS interfaces http://emboss.sourceforge.net/interfaces/ Command line: Windows, Cygwin Java: –Jemboss (needs java web start)‏ PERL and other scripts: –Bio::Emboss ModuleBio::Emboss –BioPerl EMBOSS only a partBioPerl –BioPython EMBOSS only a partBioPython Web: –EMBOSSGUI (needs Apache or other webserver)‏ –Pise –W2H –wEMBOSS Other GUIs: –StadenStaden –Kaptain (KDE2)‏Kaptain

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51 http://bioinfo.icgeb.res.in/EMBOSS

52 01/20/10 11/01/2015 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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54 EMBOSS for UNIX Download EMBOSS (ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.1.0.tar.gz )‏ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.1.0.tar.gz or from course website: http://192.168.81.55 gzip –d EMBOSS-6.1.0.tar.gz tar xvf EMBOSS-6.1.0.tar cd EMBOSS-6.1.0./configure make su (to login as root)‏ make install cntrl-D (to log off as root)‏ 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

55 01/20/10 11/01/2015 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

56 01/20/10 11/01/2015 Making own customized DBs Retrieve sequences of interests or whole dbs dbiflat -idformat swiss -dbname dgdb.dat -directory. -release 1.0 -date 05/10/05 -fields AC -verbose Modify emboss.ini in windows or.embossrc file in unix to include information about the new db


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