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| === Liz's Notes ===
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| [[E. coli genomes]]
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| [[Mauve stuff]]
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| [[Mr Bayes stuff]]
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| [[SAM]]
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|
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| = Useful links =
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| Cytoscape with Power Plugin (via Java WebStart) [http://www.biotec.tu-dresden.de/schroeder/group/powergraphs/cytoscape_webstart/cy1_powergraphsonly.jnlp]
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| = Running Java Apps =
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| Currently it appears that only version 1.4.2 of the JRE (Java Runtime Environment) is installed, which is not suitable for all applications. To use the newer version of JRE, you need to specify the full path to the java executable that is installed in the home directory e.g. instead of
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| java app.jar
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| use
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| /home/e.skippington/Programs/java/jre1.6.0_07/bin/java app.jar
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| This has been temporarily fixed by creating a symlink in ~/bin/ of java pointing to the new version of java.
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| = Running Java WebApps =
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| The latest JRE has been installed, but only the 32 bit version, so a separate 32 bit version of firefox has been installed to use the latest 32 bit version of the JRE. The 32 bit, new JRE firefox is at:
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| /usr/lib/firefox-3.0.1/firefox
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| and a symlink called firefox32 has been created to point to it.
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| = Running power graph Program =
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| Run the power graph program by something like:
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| java -Xmx1024M -jar Oog.jar -convert -inputfiles=edg -output=bbl -v -writeLog=0 -sortbyfilesize -checkequality -minsim=0.0 -min_max=1 -useGlobalClustering=1 -useGreedyClustering=1
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| Use the following line for help:
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| java -Xmx1024M -jar Oog.jar -?
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| = Making metabolic networks =
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| Metabolic data collected from KEGG 20/4/2009
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| ftp://ftp.genome.jp/pub/kegg
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| /home/e.skippington/Phd/Network/KEGG_metabolic_networks
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| wget ftp://ftp.genome.jp/pub/kegg/ligand/reaction/reaction.lst
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| wget ftp://ftp.genome.jp/pub/kegg/ligand/reaction/reaction_name.lst
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| = Installing MCL package =
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| download mcl-latest.tar.gz from http://www.micans.org/mcl/src/ to /home/e.skippington/Programs/MCL
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| tar xzf mcl-latest.tar.gz
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| ./configure --enable-blast
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| make
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| make prefix=/home/e.skippington/MCL_test/ install
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| Now the mcl executable is in /home/e.skippington/MCL_test/bin
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| Check the PATH variable:
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| echo $PATH
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| Need to append /home/e.skippington/MCL_test/bin to the path, do this by editing .bashrc in my home directory
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| ~cd
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| ls -la
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| vim .bashrc
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| Add the following line to the file:
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| PATH=$PATH:/home/e.skippington/MCL_test/bin; export PATH
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| vim mcxdeblast
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| Change the first line to:
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| #!/usr/bin/perl -w
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| = Running MCL package =
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| mcxdeblast --m9 --line-mode=abc --out=- all_16_ecoli.m9 | mcl - --abc -o all_16_e.coli.clus
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| I edited the blast results for an e-evalue cutoff of 0.01 and then ran the mcl again at different inflation parameters
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| mcxdeblast --m9 --line-mode=abc --out=- all_16_ecoli_w_cutoff.m9 | mcl - --abc -I 1.2 -o all_16_e.coli_12.clus
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| mcxdeblast --m9 --line-mode=abc --out=- all_16_ecoli_w_cutoff.m9 | mcl - --abc -I 1.6 -o all_16_e.coli_16.clus
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| mcxdeblast --m9 --line-mode=abc --out=- all_16_ecoli_w_cutoff.m9 | mcl - --abc -I 2.0 -o all_16_e.coli_2.clus
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| mcxdeblast --m9 --line-mode=abc --out=- all_16_ecoli_w_cutoff.m9 | mcl - --abc -I 2.4 -o all_16_e.coli_2.clus
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| = BLASTp =
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| Download from ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/
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| blast-2.2.18-x64-linux.tar.gz
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| All 16 E. coli fasta files are in the directory /home/e.skippington/Phd/LGT/ecoli_fasta
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| Concatenate into one big file
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| cat AC_000091.faa NC_002655.faa NC_004337.faa NC_004741.faa NC_007606.faa NC_007946.faa NC_008258.faa NC_009800.faa NC_000913.faa NC_002695.faa NC_004431.faa NC_007384.faa NC_007613.faa NC_008253.faa NC_008563.faa NC_009801.faa > all_16_ecoli.faa
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| /home/e.skippington/Programs/BLAST/blast-2.2.18/bin/formatdb -i all_16_ecoli.faa -o T -n all_16_ecoli_db
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| /home/e.skippington/Programs/BLAST/blast-2.2.18/bin/blastpgp -i all_16_ecoli.faa -d all_16_ecoli_db -o all_ecoli.m9 -m9
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