tutorials:eccb_t2_tdg09
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| tutorials:eccb_t2_tdg09 [2012/09/06 16:30] – created romainstuder | tutorials:eccb_t2_tdg09 [2012/09/08 16:26] (current) – romainstuder | ||
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| + | ==== TDG09 ==== | ||
| + | |||
| + | === Installation === | ||
| + | |||
| + | Download from here: | ||
| + | [[http:// | ||
| + | |||
| + | [[http:// | ||
| + | < | ||
| + | unzip tdg09.zip | ||
| + | </ | ||
| + | |||
| + | === Detection of site in the Influenza Virus Hemagglutinin HA1 chain === | ||
| + | |||
| + | We would like to know which sites are important between the Hemagglutinin HA1 of the virus in Avian (genes starting with Av_) and in Human (genes starting with Hu_). | ||
| + | |||
| < | < | ||
| + | |||
| + | The execution of TDG09 with this dataset could take 20 minute or more, depending of the computation power. | ||
| Lauch TDG09 with this command (it takes time (20 minutes or more)): | Lauch TDG09 with this command (it takes time (20 minutes or more)): | ||
| + | With Linux or MacOSX, you can run the command like this: | ||
| < | < | ||
| + | |||
| + | With Windows, you need to execute the whole command: | ||
| + | < | ||
| + | java -cp lib\commons-lang-2.4.jar; | ||
| + | </ | ||
| The output is put in the file tdg.out. | The output is put in the file tdg.out. | ||
| - | We need to transform it with some unix tools: | + | We need to transform it with some unix tools (the four lines are one unique command): |
| + | (/!\ These Unix tools need Cygwin to work in Windows /!\ If you don't have Cygwin, you can continue the tutorial by skip the R part. The sites are given at the end). | ||
| < | < | ||
| - | grep " | + | grep " |
| + | | tr ' | ||
| + | | awk ' | ||
| + | | cut -d' ' -f1, | ||
| </ | </ | ||
| Line 32: | Line 60: | ||
| </ | </ | ||
| - | == Jalview | + | == Jalview |
| Load multiple alignment: H1.faa | Load multiple alignment: H1.faa | ||
| (you will need to remove the first line, as it is in Phylip format. | (you will need to remove the first line, as it is in Phylip format. | ||
| Line 40: | Line 68: | ||
| Put a vertical line a the root of the tree to split the tree in two. | Put a vertical line a the root of the tree to split the tree in two. | ||
| - | => Visualise the position of these sites | + | => Visualise the position of these sites. |
tutorials/eccb_t2_tdg09.1346949022.txt.gz · Last modified: by romainstuder
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