+++ /dev/null
- GNU GENERAL PUBLIC LICENSE
- Version 2, June 1991
-
- Copyright (C) 1989, 1991 Free Software Foundation, Inc.
- 675 Mass Ave, Cambridge, MA 02139, USA
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+++ /dev/null
-
-RIO - Phylogenomic Protein Function Analysis
-
-____________________________________________
-
-
-
-
-RIO/FORESTER : http://www.genetics.wustl.edu/eddy/forester/
-RIO webserver: http://www.rio.wustl.edu/
-
-Reference: Zmasek C.M. and Eddy S.R. (2002)
- RIO: Analyzing proteomes by automated phylogenomics using
- resampled inference of orthologs.
- BMC Bioinformatics 3:14
- http://www.biomedcentral.com/1471-2105/3/14/
-
- It is highly recommended that you read this paper before
- installing and/or using RIO. (Included in the RIO
- distribution as PDF: "RIO.pdf".)
-
-
-Preconditions: A Unix system, Java 1.2 or higher, Perl, gcc or cc,
- ... and some experience with Perl and Unix.
-
-
-
-1. Compilation
-______________
-
-
-This describes how to compile the various components of RIO.
-
-
- "gunzip RIO1.x.tar.gz"
-
- "tar -xvf RIO1.x.tar"
-
-
-
-
-in directory "RIO1.x/C":
-
- "make"
-
-
-
-in directory "RIO1.x/hmmer" (version of HMMER is "2.2g"):
-
-(if you already have a local copy of HMMER 2.2g installed, this step
-is not necessary, but in this case you need to change variables "$HMMALIGN",
-"$HMMSEARCH", "$HMMBUILD", "$HMMFETCH", and "$SFE" to point to the
-corresponding HMMER programs)
-
- "./configure"
-
- "make"
-
-
-
-in directory "RIO1.x/java" (requires JDK 1.2 or greater):
-
- "javac forester/tools/*java"
-
- "javac ATVapp.java"
-
-
-
-
-in directory "RIO1.x/puzzle_dqo":
-
- "./configure"
-
- "make"
-
-
-
-in directory "RIO1.x/puzzle_mod":
-
- "./configure"
-
- "make"
-
-
-
-in directory "RIO1.x/phylip_mod/src":
-
- "make install"
-
-
-
-
-2. Setting the variables in "RIO1.x/perl/rio_module.pm"
-_______________________________________________________
-
-
-Most global variables used in "RIO1.x/perl/rio.pl" are set in
-the perl module "RIO1.x/perl/rio_module.pm".
-This module pretty much "controls everything".
-
-It is necessary to set the variables which point to:
-
--- the rio directory itself: $PATH_TO_FORESTER
-
- (example: $PATH_TO_FORESTER = "/home/czmasek/linux/RIO1.1/";)
-
-
--- your Java virtual machine: $JAVA
-
- (example: $JAVA = "/home/czmasek/linux/j2sdk1.4.0/bin/java";)
-
-
--- a directory where temporary files can be created: $TEMP_DIR_DEFAULT
-
-
-
- Example:
- Now that $PATH_TO_FORESTER, $JAVA, $TEMP_DIR_DEFAULT are set,
- it is posssible to run rio.pl based on the example precalculated distances
- in "/example_data/":
-
- % RIO1.1/perl/rio.pl 1 A=aconitase Q=RIO1.1/LEU2_HAEIN N=QUERY_HAEIN O=out0 p I
-
- To use RIO to analyze your protein sequences, please continue setting
- variables and preparing data......
-
-
-
--- your local copy of the Pfam database (see http://pfam.wustl.edu/)
- (if only precalculated distances are being used, these variables do not
- matter):
-
- $PFAM_FULL_DIRECTORY -- the directory containing the "full" alignments
- (Pfam-A.full) see below (3.)
-
- $PFAM_SEED_DIRECTORY -- the directory containing the "seed" alignments
- (Pfam-A.seed) see below (3.)
-
- $PFAM_HMM_DB -- the Pfam HMM library file (Pfam_ls)
- see below (3.)
-
-
--- $TREMBL_ACDEOS_FILE and $SWISSPROT_ACDEOS_FILE: see below (4. and 5.).
-
-
--- list of species (SWISS-PROT codes) which can be analyzed: $SPECIES_NAMES_FILE
- (for most purposes $PATH_TO_FORESTER."data/species/tree_of_life_bin_1-4_species_list"
- should be sufficient, hence this variable does not necessarly need to be changed)
-
-
--- a default species tree in NHX format: $SPECIES_TREE_FILE_DEFAULT
- (for most purposes $PATH_TO_FORESTER."data/species/tree_of_life_bin_1-4.nhx"
- should be sufficient, hence this variable does not necessarly need to be changed)
-
-
--- Only if precalculated distances are being used:
- $MATRIX_FOR_PWD, $RIO_PWD_DIRECTORY, $RIO_BSP_DIRECTORY,
- $RIO_NBD_DIRECTORY, $RIO_ALN_DIRECTORY, and $RIO_HMM_DIRECTORY:
- please see below (6.)
-
-
-
-
-
-
-IMPORTANT: Need to redo steps 3., 4., 5., and 6. if species
- in the master species tree and/or the species list
- are added and/or changed or if a new version of Pfam is used!!
-
-
-
-
-
-3. Downloading and processing of Pfam
-_____________________________________
-
-
-
-Please note: Even if you already have a local copy of the
-Pfam database, you still need to perform steps c. through k.
-
-a. download
- - "Pfam_ls" (PFAM HMM library, glocal alignment models)
- - "Pfam-A.full" (full alignments of the curated families)
- - "Pfam-A.seed" (seed alignments of the curated families)
- [and ideally "prior.tar.gz"]
- from http://pfam.wustl.edu/ or ftp.genetics.wustl.edu/pub/eddy/pfam-x/
-
-b. "gunzip" and "tar -xvf" these downloaded files, if necessary
-
-c. create a new directory named "Full" and move "Pfam-A.full" into it
-
-d. in directory "Full" execute "RIO1.x/perl/pfam2slx.pl Pfam-A.full"
-
-e. set variable $PFAM_FULL_DIRECTORY in "RIO1.x/perl/rio_module.pm"
- to point to this "Full" directory
-
-f. create a new directory named "Seed" and move "Pfam-A.seed" into it
-
-g. in directory "Seed" execute "RIO1.x/perl/pfam2slx.pl Pfam-A.seed"
-
-h. set variable $PFAM_SEED_DIRECTORY in "RIO1.x/perl/rio_module.pm"
- to point to this "Seed" directory
-
-i. execute "RIO1.x/hmmer/binaries/hmmindex Pfam_ls" (in same
- directory as "Pfam_ls") resulting in "Pfam_ls.ssi"
-
-j. set environment variable HMMERDB to point to the directory where
- "Pfam_ls" and "Pfam_ls.ssi" reside
- (for example "setenv HMMERDB /home/czmasek/PFAM7.3/")
-
-k. set variable $PFAM_HMM_DB in "RIO1.x/perl/rio_module.pm"
- to point to the "Pfam_ls" file
- (for example $PFAM_HMM_DB = "/home/czmasek/PFAM7.3/Pfam_ls";)
-
-
-
-
-4. Extraction of ID, DE, and species from a SWISS-PROT sprot.dat file
-_____________________________________________________________________
-
-
-This creates the file from which RIO will get the sequence descriptions for
-sequences from SWISS-PROT.
-(RIO1.x/data/ does not contain an example for this, since SWISS-PROT is
-copyrighted.)
-
-
-a. download SWISS-PROT "sprotXX.dat" from
- "ftp://ca.expasy.org/databases/swiss-prot/release/"
-
-b. "extractSWISS-PROT.pl <infile> <outfile> [species list]"
-
- ("extractSWISS-PROT.pl" is in "RIO1.x/perl")
-
- example:
- "extractSWISS-PROT.pl sprot40.dat sp40_ACDEOS RIO1.x/data/species/tree_of_life_bin_1-4_species_list"
-
-c. the output file should be placed in "RIO1.x/data" and the
- variable $SWISSPROT_ACDEOS_FILE in "RIO1.x/perl/rio_module.pm" should point
- to this output.
-
-
-
-
-5. Extraction of AC, DE, and species from a TrEMBL trembl.dat file
-__________________________________________________________________
-
-
-This creates the file from which RIO will get the sequence descriptions for
-sequences from TrEMBL.
-(RIO1.x/data/ already contains an example: "trembl20_ACDEOS_1-4")
-
-a. download TrEMBL "trembl.dat.gz" from
- "ftp://ca.expasy.org/databases/sp_tr_nrdb/"
-
-b. "gunzip trembl.dat.gz"
-
-c. "extractTrembl.pl <infile> <outfile> [species list]"
-
- ("extractTrembl.pl" is in "RIO1.x/perl")
-
- example:
- "extractTrembl.pl trembl.dat trembl17.7_ACDEOS_1-4 RIO1.x/data/species/tree_of_life_bin_1-4_species_list"
-
-d. the output file should be placed in "RIO1.x/data/" and the
- variable $TREMBL_ACDEOS_FILE in "RIO1.x/perl/rio_module.pm" should point
- to this output.
-
-
-
-Now, you could go to directly to 7. to run the examples......
-
-
-
-6. Precalculation of pairwise distances (optional): pfam2pwd.pl
-_______________________________________________________________
-
-
-This step is of course only necessary if you want to use RIO on
-precalculated pairwise distances. The precalculation is time consuming
-(range of one or two weeks on ten processors).
-It is best to run it on a few machines, dividing up the input data.
-
-The program to do this, is "RIO1.x/perl/pfam2pwd.pl".
-
-Please note: "pfam2pwd.pl" creates a logfile in the same directory
- where is places the pairwise distance output ($MY_RIO_PWD_DIRECTORY).
-
-
-
-The following variables in "RIO1.x/perl/pfam2pwd.pl" need to be set
-("pfam2pwd.pl" gets most of its information from "rio_module.pm"):
-
-
-"$MY_PFAM_FULL_DIRECTORY":
- This is the directory where the Pfam full alignments reside, processed
- as described in 3.a to 3.d.
-
-
-
-"$ALGNS_TO_USE_LIST_FILE":
- If left empty, all alignments in $MY_PFAM_FULL_DIRECTORY are being
- used the calculate pairwise distances from.
- If this points to a file listing names of Pfam alignments,
- only those listed are being used.
- The file can either be a simple new-line deliminated list, or can have
- the same format as the "Summary of changes" list
- ("FI PF03214 RGP NEW SEED HMM_ls HMM_fs FULL DESC")
- which is part of the Pfam distribution.
- One purpose of this is to use the list of "too large" alignments
- in the logfile produced by "pfam2pwd.pl" to run "pfam2pwd.pl" with
- a smaller species list (as can be set with "$MY_SPECIES_NAMES_FILE")
- on large alignments.
-
-
-
-"$MY_SPECIES_NAMES_FILE" -- Dealing with too large alignments:
-
- This is most important. It determines the species whose sequences
- are being used (sequences from species not listed in $MY_SPECIES_NAMES_FILE
- are ignored). Normally, one would use the same list as RIO uses
- ($SPECIES_NAMES_FILE in "rio_module.pm"):
-
- my $MY_SPECIES_NAMES_FILE = $SPECIES_NAMES_FILE;
-
- For certain large families (such as protein kinases, one must use
- a species file which contains less species in order to be able to finish
- the calculations in reasonable time:
-
- my $MY_SPECIES_NAMES_FILE = $PATH_TO_FORESTER."data/tree_of_life_bin_1-4_species_list_NO_RAT_RABBIT_MONKEYS_APES_SHEEP_GOAT_HAMSTER
-
- An additional way to reduce the number of sequences in an alignment is
- to only use sequences originating from SWISS-PROT. This is done by
- placing the following line of code into pfam2pwd.pl:
-
- $TREMBL_ACDEOS_FILE = $PATH_TO_FORESTER."data/NO_TREMBL";
-
-
-
-"$MY_RIO_PWD_DIRECTORY",
-"$MY_RIO_BSP_DIRECTORY",
-"$MY_RIO_NBD_DIRECTORY",
-"$MY_RIO_ALN_DIRECTORY",
-"$MY_RIO_HMM_DIRECTORY":
- These determine where to place the output.
- After all the data has been calculated, the corresponding variables
- in RIO1.x/perl/rio_module.pm ("$RIO_PWD_DIRECTORY", etc.) need to be set
- so that they point to the appropriate values. Having different variables
- allows to precalculate distances and at the same time use RIO on
- previously precalculated distances.
-
-
-
-"$MY_TEMP_DIR":
- A directory to create temporary files in.
-
-
-
-"$MIN_SEQS":
- Alignments in which the number of sequences after pruning (determined
- by "$MY_SPECIES_NAMES_FILE") is lower than $MIN_SEQS, are ignored
- (no calculation of pwds).
-
-
-
-"$MAX_SEQS":
- Alignments in which the number of sequences after pruning (determined
- by "$MY_SPECIES_NAMES_FILE") is greater than $MAX_SEQS, are ignored
- (no calculation of pwds).
-
-
-
-"$MY_SEED":
- Seed for the random number generator for bootstrapping (must be 4n+1).
-
-
-
-"$MY_MATRIX":
- This is used to choose the model to be used for the (ML)
- distance calculation:
- 0 = JTT
- 2 = BLOSUM 62
- 3 = mtREV24
- 5 = VT
- 6 = WAG
- PAM otherwise
- After all the data has been calculated, variable "$MATRIX_FOR_PWD"
- in RIO1.x/perl/rio_module.pm needs to be set to the same value.
-
-
-
-Once pairwise distances are calculated, the following variables in
-"rio_module.pm" need to be set accordingly:
-$MATRIX_FOR_PWD : corresponds to $MY_MATRIX in pfam2pwd.pl
-$RIO_PWD_DIRECTORY : corresponds to $MY_RIO_PWD_DIRECTORY in pfam2pwd.pl
-$RIO_BSP_DIRECTORY : corresponds to $MY_RIO_BSP_DIRECTORY in pfam2pwd.pl
-$RIO_NBD_DIRECTORY : corresponds to $MY_RIO_NBD_DIRECTORY in pfam2pwd.pl
-$RIO_ALN_DIRECTORY : corresponds to $MY_RIO_ALN_DIRECTORY in pfam2pwd.pl
-$RIO_HMM_DIRECTORY : corresponds to $MY_RIO_HMM_DIRECTORY in pfam2pwd.pl
-...of course, if Pfam has been updated, the corresponding variables in rio_module.pm
-($PFAM_FULL_DIRECTORY, etc.) need to be updated, too.
-
-
-
-
-
-
-IMPORTANT: Need to redo steps 3., 4., 5., and 6. if species
- in the master species tree and/or the species list
- are added and/or changed or if a new version of Pfam is used!
-
-
-
-
-7. Example of a phylogenomic analysis using "rio.pl"
-____________________________________________________
-
-
-Without using precalculated distances (for this, all the variables above
-need to point to the correct loctions, in particular to your local and processed
-Pfam database):
-
- % RIO1.1/perl/rio.pl 3 A=/path/to/my/pfam/Full/aconitase H=aconitase Q=RIO1.1/LEU2_HAEIN N=QUERY_HAEIN O=out3 p I C E
-
-
-
-Without using precalculated distances (for this, all the variables above
-need to point to the correct loctions, in particular to your local and processed
-Pfam database) using a query sequence which is already in the alignment:
-
- % RIO1.1/perl/rio.pl 4 A=/path/to/my/pfam/Full/aconitase N=LEU2_LACLA/5-449 O=out4 p I C E
-
-
-
-Using the example precalculated distances in "/example_data/"
-($RIO_PWD_DIRECTORY, etc. need to point to $PATH_TO_FORESTER."example_data/"):
-
- % RIO1.1/perl/rio.pl 1 A=aconitase Q=RIO1.1/LEU2_HAEIN N=QUERY_HAEIN O=out1 p I C E
-
-
-
-Using a query sequence which is already in the precalculated distances in "/example_data/"
-($RIO_PWD_DIRECTORY, etc. need to point to $PATH_TO_FORESTER."example_data/"):
-
- % RIO1.1/perl/rio.pl 2 A=aconitase N=LEU2_LACLA/5-449 O=out2 p I C E
-
-
-
-for detailed instructions on how to use rio.pl see the source code,
-or type "rio.pl" without any arguments
-
-
-
-
-Christian Zmasek
-zmasek@genetics.wustl.edu
-05/26/02
-
git://source.jalview.org / jalview.git / commitdiff