Bio::Tools::Run::Alignment::TCoffee - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program # Build a tcoffee alignment factory @params = ('ktuple' => 2, 'matrix' => 'BLOSUM'); $factory = new Bio::Tools::Run::Alignment::TCoffee (@params); # Pass the factory a list of sequences to be aligned. $inputfilename = 't/cysprot.fa'; # $aln is a SimpleAlign object. $aln = $factory->align($inputfilename); # or where @seq_array is an array of Bio::Seq objects $seq_array_ref = \@seq_array; $aln = $factory->align($seq_array_ref); # Or one can pass the factory a pair of (sub)alignments #to be aligned against each other, e.g.: # where $aln1 and $aln2 are Bio::SimpleAlign objects. $aln = $factory->profile_align($aln1,$aln2); # Or one can pass the factory an alignment and one or more # unaligned sequences to be added to the alignment. For example: # $seq is a Bio::Seq object. $aln = $factory->profile_align($aln1,$seq); There are various additional options and input formats available. See the DESCRIPTION section that follows for additional details. Note: this DESCRIPTION only documents the (Bio)perl interface to TCoffee. There are a number of possible parameters one can pass in TCoffee. One should really read the online manual for the best explaination of all the features. See http://igs-server.cnrs-mrs.fr/~cnotred/Documentation/t_coffee/t_coffee_doc.html These can be specified as parameters when instantiating a new TCoffee object, or through get/set methods of the same name (lowercase).

IN
Title : IN Description : (optional) input filename, this is specified when align so should not use this directly unless one understand TCoffee program very well.

TYPE
Title : TYPE Args : [string] DNA, PROTEIN Description : (optional) set the sequence type, guessed automatically so should not use this directly

PARAMETERS
Title : PARAMETERS Description : (optional) Indicates a file containing extra parameters

EXTEND
Title : EXTEND Args : 0, 1, or positive value Default : 1 Description : Flag indicating that library extension should be carried out when performing multiple alignments, if set to 0 then extension is not made, if set to 1 extension is made on all pairs in the library. If extension is set to another positive value, the extension is only carried out on pairs having a weigth value superior to the specified limit.

DP_NORMALISE
Title : DP_NORMALISE Args : 0 or positive value Default : 1000 Description : When using a value different from 0, this flag sets the score of the highest scoring pair to 1000.

DP_MODE
Title : DP_MODE Args : [string] gotoh_pair_wise, myers_miller_pair_wise, fasta_pair_wise cfasta_pair_wise Default : cfast_fair_wise Description : Indicates the type of dynamic programming used by the program gotoh_pair_wise : implementation of the gotoh algorithm (quadratic in memory and time) myers_miller_pair_wise : implementation of the Myers and Miller dynamic programming algorithm ( quadratic in time and linear in space). This algorithm is recommended for very long sequences. It is about 2 time slower than gotoh. It only accepts tg_mode=1. fasta_pair_wise: implementation of the fasta algorithm. The sequence is hashed, looking for ktuples words. Dynamic programming is only carried out on the ndiag best scoring diagonals. This is much faster but less accurate than the two previous. cfasta_pair_wise : c stands for checked. It is the same algorithm. The dynamic programming is made on the ndiag best diagonals, and then on the 2*ndiags, and so on until the scores converge. Complexity will depend on the level of divergence of the sequences, but will usually be L*log(L), with an accuracy comparable to the two first mode ( this was checked on BaliBase).

KTUPLE
Title : KTUPLE Args : numeric value Default : 1 or 2 (1 for protein, 2 for DNA ) Description : Indicates the ktuple size for cfasta_pair_wise dp_mode and fasta_pair_wise. It is set to 1 for proteins, and 2 for DNA. The alphabet used for protein is not the 20 letter code, but a mildly degenerated version, where some residues are grouped under one letter, based on physicochemical properties: rk, de, qh, vilm, fy (the other residues are not degenerated).

NDIAGS
Title : NDIAGS Args : numeric value Default : 0 Description : Indicates the number of diagonals used by the fasta_pair_wise algorithm. When set to 0, n_diag=Log (length of the smallest sequence)

DIAG_MODE
Title : DIAG_MODE Args : numeric value Default : 0 Description : Indicates the manner in which diagonals are scored during the fasta hashing. 0 indicates that the score of a diagonal is equal to the sum of the scores of the exact matches it contains. 1 indicates that this score is set equal to the score of the best uninterrupted segment 1 can be useful when dealing with fragments of sequences.

SIM_MATRIX
Title : SIM_MATRIX Args : string Default : vasiliky Description : Indicates the manner in which the amino acid is being degenerated when hashing. All the substitution matrix are acceptable. Categories will be defined as sub-group of residues all having a positive substitution score (they can overlap). If you wish to keep the non degenerated amino acid alphabet, use 'idmat'

MATRIX
Title : MATRIX Args : Default : Description : This flag is provided for compatibility with ClustalW. Setting matrix = 'blosum' is equivalent to -in=Xblosum62mt , -matrix=pam is equivalent to in=Xpam250mt . Apart from this, the rules are similar to those applying when declaring a matrix with the -in=X fl

GAPOPEN
Title : GAPOPEN Args : numeric Default : 0 Description : Indicates the penalty applied for opening a gap. The penalty must be negative. If you provide a positive value, it will automatically be turned into a negative number. We recommend a value of 10 with pam matrices, and a value of 0 when a library is used.

GAPEXT
Title : GAPEXT Args : numeric Default : 0 Description : Indicates the penalty applied for extending a gap.

COSMETIC_PENALTY
Title : COSMETIC_PENALTY Args : numeric Default : 100 Description : Indicates the penalty applied for opening a gap. This penalty is set to a very low value. It will only have an influence on the portions of the alignment that are unalignable. It will not make them more correct, but only more pleasing to the eye ( i.e. Avoid stretches of lonely residues). The cosmetic penalty is automatically turned off if a substitution matrix is used rather than a library.

TG_MODE
Title : TG_MODE Args : 0,1,2 Default : 1 Description : (Terminal Gaps) 0: indicates that terminal gaps must be panelized with a gapopen and a gapext penalty. 1: indicates that terminal gaps must be penalized only with a gapext penalty 2: indicates that terminal gaps must not be penalized.

WEIGHT
Title : WEIGHT Args : sim or sim_<matrix_name or matrix_file> or integer value Default : sim Description : Weight defines the way alignments are weighted when turned into a library. sim indicates that the weight equals the average identity within the match residues. sim_matrix_name indicates the average identity with two residues regarded as identical when their substitution value is positive. The valid matrices names are in matrices.h (pam250mt) . Matrices not found in this header are considered to be filenames. See the format section for matrices. For instance, -weight=sim_pam250mt indicates that the grouping used for similarity will be the set of classes with positive substitutions. Other groups include sim_clustalw_col ( categories of clustalw marked with :) sim_clustalw_dot ( categories of clustalw marked with .) Value indicates that all the pairs found in the alignments must be given the same weight equal to value. This is useful when the alignment one wishes to turn into a library must be given a pre-specified score (for instance if they come from a structure super-imposition program). Value is an integer: -weight=1000 Note : Weight only affects methods that return an alignment to T-Coffee, such as ClustalW. On the contrary, the version of Lalign we use here returns a library where weights have already been applied and are therefore insensitive to the -weight flag.

SEQ_TO_ALIGN
Title : SEQ_TO_ALIGN Args : filename Default : no file - align all the sequences Description : You may not wish to align all the sequences brought in by the -in flag. Supplying the seq_to_align flag allows for this, the file is simply a list of names in Fasta format. However, note that library extension will be carried out on all the sequences.

NEWTREE
Title : NEWTREE Args : treefile Default : no file Description : Indicates the name of the new tree to compute. The default will be <sequence_name>.dnd, or <run_name.dnd>. Format is Phylips tree format

USETREE
Title : USETREE Args : treefile Default : no file specified Description : This flag indicates that rather than computing a new dendrogram, t_coffee can use a pre-computed one. The tree files are in phylips format and compatible with ClustalW. In most cases, using a pre-computed tree will halve the computation time required by t_coffee. It is also possible to use trees output by ClustalW or Phylips. Format is Phylips tree format

TREE_MODE
Title : TREE_MODE Args : slow, fast, very_fast Default : very_fast Description : This flag indicates the method used for computing the dendrogram. slow : the chosen dp_mode using the extended library, fast : The fasta dp_mode using the extended library. very_fast: The fasta dp_mode using pam250mt.

QUICKTREE
Title : QUICKTREE Args : Default : Description : This flag is kept for compatibility with ClustalW. It indicates that: -tree_mode=very_fast

OUTFILE
Title : OUTFILE Args : out_aln file, default, no Default : default ( yourseqfile.aln) Description : indicates name of output alignment file

OUTPUT
Title : OUTPUT Args : format1, format2 Default : clustalw Description : Indicated format for outputting outputfile Supported formats are: clustalw_aln, clustalw: ClustalW format. gcg, msf_aln : Msf alignment. pir_aln : pir alignment. fasta_aln : fasta alignment. phylip : Phylip format. pir_seq : pir sequences (no gap). fasta_seq : fasta sequences (no gap). As well as: score_html : causes the output to be a reliability plot in HTML score_pdf : idem in PDF. score_ps : idem in postscript. More than one format can be indicated: -output=clustalw,gcg, score_html

CASE
Title : CASE Args : upper, lower Default : upper Description : triggers choice of the case for output

CPU
Title : CPU Args : value Default : 0 Description : Indicates the cpu time (micro seconds) that must be added to the t_coffee computation time.

OUT_LIB
Title : OUT_LIB Args : name of library, default, no Default : default Description : Sets the name of the library output. Default implies <run_name>.tc_lib

OUTORDER
Title : OUTORDER Args : input or aligned Default : input Description : Sets the name of the library output. Default implies <run_name>.tc_lib

SEQNOS
Title : SEQNOS Args : on or off Default : off Description : Causes the output alignment to contain residue numbers at the end of each line:

RUN_NAME
Title : RUN_NAME Args : your run name Default : Description : This flag causes the prefix <your sequences> to be replaced by <your run name> when renaming the default files.

ALIGN
Title : ALIGN Args : Default : Description : Indicates that the program must produce the alignment. This flag is here for compatibility with ClustalW

QUIET
Title : QUIET Args : stderr, stdout, or filename, or nothing Default : stderr Description : Redirects the standard output to either a file. -quiet on its own redirect the output to /dev/null.

CONVERT
Title : CONVERT Args : Default : Description : Indicates that the program must not compute the alignment but simply convert all the sequences, alignments and libraries into the format indicated with -output. This flag can also be used if you simply want to compute a library ( i.e. You have an alignment and you want to turn it into a library).

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ Email jason@chg.mc.duke.edu, schattner@alum.mit.edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

exists_tcoffee
Title : exists_tcoffee Usage : $coffeefound = Bio::Tools::Run::Alignment::TCoffee->exists_tcoffee() Function: Determine whether tcoffee program can be found on current host Example : Returns : 1 if tcoffee program found at expected location, 0 otherwise. Args : none

align
Title : align Usage : $inputfilename = 't/cysprot.fa'; $aln = $factory->align($inputfilename); or $seq_array_ref = \@seq_array; @seq_array is array of Seq objs $aln = $factory->align($seq_array_ref); Function: Perform a multiple sequence alignment Example : Returns : Reference to a SimpleAlign object containing the sequence alignment. Args : Name of a file containing a set of unaligned fasta sequences or else an array of references to Bio::Seq objects. Throws an exception if argument is not either a string (eg a filename) or a reference to an array of Bio::Seq objects. If argument is string, throws exception if file corresponding to string name can not be found. If argument is Bio::Seq array, throws exception if less than two sequence objects are in array.

profile_align
Title : profile_align Usage : Function: Perform an alignment of 2 (sub)alignments Example : Returns : Reference to a SimpleAlign object containing the (super)alignment. Args : Names of 2 files containing the subalignments or references to 2 Bio::SimpleAlign objects. Throws an exception if arguments are not either strings (eg filenames) or references to SimpleAlign objects.

_run
Title : _run Usage : Internal function, not to be called directly Function: makes actual system call to tcoffee program Example : Returns : nothing; tcoffee output is written to a temporary file $TMPOUTFILE Args : Name of a file containing a set of unaligned fasta sequences and hash of parameters to be passed to tcoffee

_setinput
Title : _setinput Usage : Internal function, not to be called directly Function: Create input file for tcoffee program Example : Returns : name of file containing tcoffee data input Args : Seq or Align object reference or input file name

_setparams
Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for tcoffee program Example : Returns : parameter string to be passed to tcoffee during align or profile_align Args : name of calling object multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program"