View source for Tools for the bioinformatics lab

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Tools for the bioinformatics lab
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Summary ...


__TOC__


==EMBOSS==

===EMBOSS installation===
;Outdated (written 2006).

===Download===
:1. navigate to the [http://emboss.sourceforge.net/download/ EMBOSS  download page on sourceforge] and read the information on the latest download there. As of this writing, the latest major release is version 3.0.
:2. Download this compressed archive.
:3. open a terminal session, navigate to your download directory and type the usual (remember to use the tab key for filename completion :-):
 gunzip ''EMBOSS-3.0.0.tar.gz''
 tar -xvf ''EMBOSS-3.0.0.tar''
 rm ''EMBOSS-3.0.0.tar''
 cd ''EMBOSS-3.0.0''

Before you begin, it may be a good idea to browse through some of the files that have been downloaded to get you oriented, these include:
 INSTALL
 KNOWN_BUGS  (this is an empty file in this release)
 README

===Compile===
EMBOSS requires a number of system specific options to be set and thus will '''generate''' its makefile before it can be used, by running the program <tt>configure</tt>. Type:
 configure
Then type
 make
Compilation will run for some time. Then type
 sudo make install
and finally
 make clean

===Test===
First see whether installation was successful in principle. Typing
 ls /usr/local/share/EMBOSS/data/
should list some of the data resources that have been installed and where they are located. Now open a new shell and type
 tfm needle
You should see man-like help pages for EMBOSS commands. In fact <tt>tfm</tt> is itself an EMBOSS command, it runs a program that formats and displays help files. If the above works, it tells you two things: (i) that EMBOSSS programs have been compiled and installed, and (ii) that the installation is on your <tt>PATH</tt>.

Next, try a simple pairwise alignment. Create two sequence files (2):

;HBA.fa
 >HBA_HUMAN
 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH
 GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL
 LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

;HBB.fa
 >HBB_HUMAN
 VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLST
 PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP
 ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

and type the following comand (note: I am using the multiline command character "\" here to ''wrap'' the command, but it could also be type all on one line:

 needle -asequence HBA.fa -bsequence HBB.fa \
 -gapopen 10.0 -gapextend 0.5 -datafile EBLOSUM62 \
 -outfile test.ali
Then typing 
 cat test.ali
should give you the following output:

 ########################################
 # Program: needle
 # Rundate: Sun Mar 02 2006 14:32:03
 # Align_format: srspair
 # Report_file: test2.ali
 ########################################
 
 #=======================================
 #
 # Aligned_sequences: 2
 # 1: HBA_HUMAN
 # 2: HBB_HUMAN
 # Matrix: EBLOSUM62
 # Gap_penalty: 10.0
 # Extend_penalty: 0.5
 #
 # Length: 148
 # Identity:      63/148 (42.6%)
 # Similarity:    88/148 (59.5%)
 # Gaps:           9/148 ( 6.1%)
 # Score: 290.5
 # 
 #
 #=======================================
 
 HBA_HUMAN          1 -VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DL     48
                       .|:|.:|:.|.|.||||  :..|.|.|||.|:.:.:|.|:.:|..| ||
 HBB_HUMAN          1 VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDL     48
 
 HBA_HUMAN         49 S-----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRV     93
                      |     .|:.:||.|||||..|.::.:||:|::....:.||:||..||.|
 HBB_HUMAN         49 STPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHV     98
 
 HBA_HUMAN         94 DPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR    141
                      ||.||:||.:.|:..||.|...||||.|.|:..|.:|.|:..|..||.
 HBB_HUMAN         99 DPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH    146
 
 
 #---------------------------------------
 #---------------------------------------
 


----
===Notes===
(1) In these notes, I assume the "." directory is on your <tt>PATH</tt> - if it is not, you may have to prepend "./" to commands to tell the operating system the executable file for the command is in your current working directory.

(2) My favorite quick and dirty way to create a text file (e.g. called <tt>file.txt</tt>) based on something I can copy and paste, is to type
 cat > file.txt
then I simply paste the contents and close the file with <tt>&lt;ctrl&gt;d</tt>. Ask me if you don't understand how this works.


==Phylip==

===Phylip installation===
;Outdated (written 2006).

;Download
:1. navigate to the [http://evolution.genetics.washington.edu/phylip/getme.html download section of the PHYLIP homepage].
:2. read the instructions ... depending on your platform, there may be an easier way than installing from source. Neverthless, since this is the most general, here I will compile from source. 
:2. Download the compressed archive.
:3. open a terminal session, navigate to your download directory and type the usual (remember to use the tab key for filename completion :-):
 gunzip ''phylip-3.65.tar.gz''
 tar -xvf ''phylip-3.65.tar''
 cd ''phylip3.65/src''

;Compile
PHYLIP uses graphical routines in some of its programs. These have to be linked against X-terminal libraries. The Makefile should know where to find them on your system. On my Mac I need to type <tt>make&nbsp;-f&nbsp;Makefile.osx&nbsp;install</tt>, on your Linux boxes, it should simply work in the standard way:
Type:
 make install
On my system the whole package compiles with almost no nag. Bravo Joe Felsenstein, for understanding the benefit of writing plain, robust, portable code. 

The excutables are being put into the directory <tt>''distribution''.exe</tt> and as usual  have to be put on on your <tt>PATH</tt>, your <tt>PATH</tt> changed or (my preferred way) copied to <tt>/usr/local/bin</tt>.

 cd ..
 ll exe
 sudo cp exe/* /usr/local/bin

;Test
...
 
;That should be all


==Clustal==

This is provided for reference, but you '''must'''know that CLUSTAL is an inferior algorithm for protein MSA.

===Clustal installation===
;Outdated (written 2006).


;Download
:1. navigate to the [http://www.ebi.ac.uk/clustalw/index.html CLUSTAL homepage at the EBI]:
:2. at the top of the page, there are icons for Mac and Linux installations (Windows too). Clicking on the Apple folder downloads the latest precompiled Max OS X version (clustalw1.82.mac-osx.tar.gz as of this writing). '''Don't do this even if you are on a Mac! (1)'''. Clicking  on the folder with the penguin icon takes you to an ftp directory which also contains sources for parallel architecture machines. clustalw1.83.UNIX.tar.gz appears to be the current UNIX version as of this writing. Download this compressed archive.
:3. open a terminal session, navigate to your download directory and type the usual (remember to use the tab key for filename completion :-):
 gunzip ''clustalw1.83.UNIX.tar.gz''
 tar -xvf ''clustalw1.83.UNIX.tar''
 cd ''clustalw1.83''

;Compile
Type:
 make
On my system this compiles with one warning about a redefined symbol which does not appear to be of any consequence. The executable <tt>'''clustalw'''</tt> is being generated. The <tt>makefile</tt> is not really up to standard since it has no provisions for  <tt>make test</tt> or  <tt>make install</tt>.  So we will run our own very simple test and installation. Remove the object files (they are no longer needed after being compiled and linked into the executable. Type
 make clean
Since you also do not require the C sources anymore and could download them from the server at anytime if you did, you may also type
 rm *.c *.h
to clean up the directory.


;Test
The directory contains a test input by the name <tt>'''globin.pep'''</tt>. These are globin sequences in the dated PIR format. I have transformed them into Fasta format below. Copy the following sequences and save them in a file by the name <tt>'''globin.mfa'''</tt>.

 >HBB_HUMAN
 VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLST
 PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP
 ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH
 
 >HBB_HORSE
 VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSN
 PGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDP
 ENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH
 
 >HBA_HUMAN
 VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH
 GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKL
 LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR
 
 >HBA_HORSE
 VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSH
 GSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKL
 LSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR
 
 >MYG_PHYCA
 VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLK
 TEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIP
 IKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELG
 YQG
 
 >GLB5_PETMA
 PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
 FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
 LSGKHAKSFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSAY
 
 >LGB2_LUPLU
 GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGT
 SEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSK
 GVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELAIVIKKEMN
 DAA
 
Now type
 clustalw -options
to verify that the program runs in principle (this will print a list of the commandline options). Then run the following command:
 clustalw -infile=globin.mfa
This should have created the two files <tt>'''globin.aln'''</tt> and <tt>'''globin.dnd'''</tt> with the following contents:
;<tt>globin.aln</tt>
 CLUSTAL W (1.83) multiple sequence alignment
 
 
 HBB_HUMAN       --------VHLTPEEKSAVTALWGKVN--VDEVGGEALGRLLVVYPWTQRFFESFGDLST
 HBB_HORSE       --------VQLSGEEKAAVLALWDKVN--EEEVGGEALGRLLVVYPWTQRFFDSFGDLSN
 HBA_HUMAN       ---------VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS-
 HBA_HORSE       ---------VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHF-DLS-
 GLB5_PETMA      PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
 MYG_PHYCA       ---------VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKT
 LGB2_LUPLU      --------GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSE
                           *:  :   :   *  .           :  .:   * :   *  :   . 
 
 HBB_HUMAN       PDAVMGNPKVKAHGKKVLGAFSDGLAHLDN-----LKGTFATLSELHCDKLHVDPENFRL
 HBB_HORSE       PGAVMGNPKVKAHGKKVLHSFGEGVHHLDN-----LKGTFAALSELHCDKLHVDPENFRL
 HBA_HUMAN       ----HGSAQVKGHGKKVADALTNAVAHVDD-----MPNALSALSDLHAHKLRVDPVNFKL
 HBA_HORSE       ----HGSAQVKAHGKKVGDALTLAVGHLDD-----LPGALSNLSDLHAHKLRVDPVNFKL
 GLB5_PETMA      ADQLKKSADVRWHAERIINAVNDAVASMDDT--EKMSMKLRDLSGKHAKSFQVDPQYFKV
 MYG_PHYCA       EAEMKASEDLKKHGVTVLTALGAILKKKGH-----HEAELKPLAQSHATKHKIPIKYLEF
 LGB2_LUPLU      VP--QNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKG-VADAHFPV
                       . .:: *.  :   .                  :  *.  *  .  :    : .
 
 HBB_HUMAN       LGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------
 HBB_HORSE       LGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH------
 HBA_HUMAN       LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------
 HBA_HORSE       LSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR------
 GLB5_PETMA      LAAVIADTVAAG---------DAGFEKLMSMICILLRSAY-------
 MYG_PHYCA       ISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
 LGB2_LUPLU      VKEAILKTIKEVVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA---
                 :   :  .:            ...       .   :         

;<tt>globin.dnd</tt>
 (
 (
 (
 (
 HBB_HUMAN:0.08080,
 HBB_HORSE:0.08359)
 :0.23578,
 (
 HBA_HUMAN:0.06516,
 HBA_HORSE:0.05541)
 :0.19444)
 :0.07579,
 GLB5_PETMA:0.37023)
 :0.02699,
 MYG_PHYCA:0.37220,
 LGB2_LUPLU:0.47094);
 

;Install
To be able to run clustal from the commandline, it needs to be in a directory on your <tt>PATH</tt>. This could either be done by putting the program into a directory on the path, or by modifying the <tt>PATH</tt> appropriately. My preferred way to do this is to keep the executables in <tt>/usr/local/bin</tt>. First I copy the executable to the directory in which I keep my locally installed programs (''type'' <tt>echo $PATH</tt> ''if you are not sure that this directory exists and is on your path on your own machine'').

 sudo cp clustalw /usr/local/bin
Finally I copy the help file into the same directory, so <tt>clustalw</tt> can find it:
 sudo cp clustalw_help /usr/local/bin

;That should be all


----
;Notes
:(1) The Mac Os X archives contain two compiled binaries and an unintelligible readme.html. The binaries appear to run but miss any helpfiles or documentation. This is useless pseudosupport, the only thing you save yourself is the trivial task of compiling the executables but when you compile from source at least you get the complete kit and everything is nicely in its place.


&nbsp;
==T-Coffee==


===T-Coffee installation===
;Outdated (written 2006).

;Download
:1. navigate to the [http://www.igs.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html T-Coffee project homepage]. Find the link to the latest Unix or Windows version (3.79 as of this writing).:
:2. Download this compressed archive.
:3. open a terminal session, navigate to your download directory and type the usual (remember to use the tab key for filename completion :-):
 gunzip ''T-COFFEE_distribution_Version_3.79.tar.gz''
 tar -xvf ''T-COFFEE_distribution_Version_3.79.tar''
 cd ''T-COFFEE_distribution_Version_3.79''

;Compile
T-Coffee provides an installation file for its standard installation. Type
 install
On my system this compiles with a spate of warnings about incompatible implicit declaration of a built-in function, but the tests appear to run oK. The executable <tt>'''t_coffee'''</tt> was generated and moved to the directory <tt>bin/</tt>. Remove the object files (they are no longer needed after being compiled and linked into the executable. Type
 cd t_coffee_source
 make clean
 cd .. 

;Install
To be able to run T-Coffee from the commandline, it needs to be in a directory on your <tt>PATH</tt>. This could either be done by putting the program into a directory on the path, or by modifying the <tt>PATH</tt> appropriately. My preferred way to do this is to keep the executables in <tt>/usr/local/bin</tt>. First I copy the executable to the directory in which I keep my locally installed programs (''type'' <tt>echo $PATH</tt> ''if you are not sure that this directory exists and is on your path on your own machine'').

 sudo cp bin/t_coffee /usr/local/bin

;Test
As a final test, type the following (this assumes you are still in the main directory of the distribution:

 t_coffee test/test.pep -in fast_pair -outfile=test.aln -outorder=input>/dev/null
 cat test.aln

should produce the following output
 CLUSTAL FORMAT for T-COFFEE Version_3.79, CPU=0.16 sec, SCORE=24, Nseq=5, Len=87 
 
 1aboA           ---nlf-valydfvasgdntlsitkgeklrvlg-----------ynhnge--wceaqtkn
 1ycsB           --kgvi-yalwdyepqnddelpmkegdcmtiih-----------rededeiewwwarlnd
 1pht            ---gyqyralydykkereedidlhlgdiltvnkgslvalgfsdgqearpeeigwlngyne
 1ihvA           -nfrvy-y--------rdsrdpvwkgpakllwk-----------gegavv-----iqdns
 1vie            drvrkk-s--------gaawqgqivgwyctnlt-----------pegyaves-----eah
                                          *                   :              
 
 1aboA           gq-----------gwvpsnyitpvn--
 1ycsB           ke-----------gyvprnllglyp--
 1pht            ttgergdfpgtyveyigrkkisp----
 1ihvA           di-----------kvvprrkakiird-
 1vie            pg-----------svqiypvaalerin
                                            

;That should be all


&nbsp;
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==Exercises==
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<section end=exercises />


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==Notes==
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==Further reading and resources==
<!-- {{#pmid:21627854}} -->
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&nbsp;
[[Category:Applied_Bioinformatics]]
</div>