Bio::Align::AlignI - An interface for describing sequence alignments. # get a Bio::Align::AlignI somehow - typically using Bio::AlignIO system # some descriptors print $aln->length, "\n"; print $aln->no_residues, "\n"; print $aln->is_flush, "\n"; print $aln->no_sequences, "\n"; print $aln->percentage_identity, "\n"; print $aln->consensus_string(50), "\n"; # find the position in the alignment for a sequence location $pos = $aln->column_from_residue_number('1433_LYCES', 14); # = 6; # extract sequences and check values for the alignment column $pos foreach $seq ($aln->each_seq) { $res = $seq->subseq($pos, $pos); $count{$res}++; } foreach $res (keys %count) { printf "Res: %s Count: %2d\n", $res, $count{$res}; } This interface describes the basis for alignment objects.

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Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org Ewan Birney, birney@ebi.ac.uk Heikki Lehvaslaiho, heikki@ebi.ac.uk The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ These methods modify the MSE by adding, removing or shuffling complete sequences.

add_seq
Title : add_seq Usage : $myalign->add_seq($newseq); Function : Adds another sequence to the alignment. *Does not* align it - just adds it to the hashes. Returns : nothing Argument : a Bio::LocatableSeq object order (optional) See Bio::LocatableSeq for more information.

remove_seq
Title : remove_seq Usage : $aln->remove_seq($seq); Function : Removes a single sequence from an alignment Returns : Argument : a Bio::LocatableSeq object

purge
Title : purge Usage : $aln->purge(0.7); Function: Removes sequences above whatever %id. This function will grind on large alignments. Beware! (perhaps not ideally implemented) Example : Returns : An array of the removed sequences Argument:

sort_alphabetically
Title : sort_alphabetically Usage : $ali->sort_alphabetically Function : Changes the order of the alignemnt to alphabetical on name followed by numerical by number. Returns : Argument : Methods returning one or more sequences objects.

each_seq
Title : each_seq Usage : foreach $seq ( $align->each_seq() ) Function : Gets an array of Seq objects from the alignment Returns : an array Argument :

each_alphabetically
Title : each_alphabetically Usage : foreach $seq ( $ali->each_alphabetically() ) Function : Returns an array of sequence object sorted alphabetically by name and then by start point. Does not change the order of the alignment Returns : Argument :

each_seq_with_id
Title : each_seq_with_id Usage : foreach $seq ( $align->each_seq_with_id() ) Function : Gets an array of Seq objects from the alignment, the contents being those sequences with the given name (there may be more than one) Returns : an array Argument : a seq name

get_seq_by_pos
Title : get_seq_by_pos Usage : $seq = $aln->get_seq_by_pos(3) # third sequence from the alignment Function : Gets a sequence based on its position in the alignment. Numbering starts from 1. Sequence positions larger than no_sequences() will thow an error. Returns : a Bio::LocatableSeq object Argument : positive integer for the sequence osition The result of these methods are horizontal or vertical subsets of the current MSE.

select
Title : select Usage : $aln2 = $aln->select(1, 3) # three first sequences Function : Creates a new alignment from a continuous subset of sequences. Numbering starts from 1. Sequence positions larger than no_sequences() will thow an error. Returns : a Bio::SimpleAlign object Argument : positive integer for the first sequence positive integer for the last sequence to include (optional)

select_noncont
Title : select_noncont Usage : $aln2 = $aln->select_noncont(1, 3) # first and 3rd sequences Function : Creates a new alignment from a subset of sequences. Numbering starts from 1. Sequence positions larger than no_sequences() will thow an error. Returns : a Bio::SimpleAlign object Args : array of integers for the sequences

slice
Title : slice Usage : $aln2 = $aln->slice(20, 30) Function : Creates a slice from the alignment inclusive of start and end columns. Sequences with no residues in the slice are excluded from the new alignment and a warning is printed. Slice beyond the length of the sequence does not do padding. Returns : a Bio::SimpleAlign object Argument : positive integer for start column positive integer for end column These methods affect characters in all sequences without changeing the alignment.

map_chars
Title : map_chars Usage : $ali->map_chars('\.','-') Function : Does a s/$arg1/$arg2/ on the sequences. Useful for gap characters Notice that the from (arg1) is interpretted as a regex, so be careful about quoting meta characters (eg $ali->map_chars('.','-') wont do what you want) Returns : Argument : 'from' rexexp 'to' string

uppercase
Title : uppercase() Usage : $ali->uppercase() Function : Sets all the sequences to uppercase Returns : Argument :

match_line
Title : match_line() Usage : $align->match_line() Function : Generates a match line - much like consensus string except that a line indicating the '*' for a match. Argument : (optional) Match line characters ('*' by default) (optional) Strong match char (':' by default) (optional) Weak match char ('.' by default)

match
Title : match() Usage : $ali->match() Function : Goes through all columns and changes residues that are identical to residue in first sequence to match '.' character. Sets match_char. USE WITH CARE: Most MSE formats do not support match characters in sequences, so this is mostly for output only. NEXUS format (Bio::AlignIO::nexus) can handle it. Returns : 1 Argument : a match character, optional, defaults to '.'

unmatch
Title : unmatch() Usage : $ali->unmatch() Function : Undoes the effect of method match. Unsets match_char. Returns : 1 Argument : a match character, optional, defaults to '.' Methods for setting and reading the MSE attributes. Note that the methods defining character semantics depend on the user to set them sensibly. They are needed only by certain input/output methods. Unset them by setting to an empty string ('').

id
Title : id Usage : $myalign->id("Ig") Function : Gets/sets the id field of the alignment Returns : An id string Argument : An id string (optional)

missing_char
Title : missing_char Usage : $myalign->missing_char("?") Function : Gets/sets the missing_char attribute of the alignment It is generally recommended to set it to 'n' or 'N' for nucleotides and to 'X' for protein. Returns : An missing_char string, Argument : An missing_char string (optional)

match_char
Title : match_char Usage : $myalign->match_char('.') Function : Gets/sets the match_char attribute of the alignment Returns : An match_char string, Argument : An match_char string (optional)

gap_char
Title : gap_char Usage : $myalign->gap_char('-') Function : Gets/sets the gap_char attribute of the alignment Returns : An gap_char string, defaults to '-' Argument : An gap_char string (optional)

symbol_chars
Title : symbol_chars Usage : my @symbolchars = $aln->symbol_chars; Function: Returns all the seen symbols (other than gaps) Returns : array of characters that are the seen symbols Argument: boolean to include the gap/missing/match characters These read only methods describe the MSE in various ways.

consensus_string
Title : consensus_string Usage : $str = $ali->consensus_string($threshold_percent) Function : Makes a strict consensus Returns : Argument : Optional treshold ranging from 0 to 100. The consensus residue has to appear at least threshold % of the sequences at a given location, otherwise a '?' character will be placed at that location. (Default value = 0%)

consensus_iupac
Title : consensus_iupac Usage : $str = $ali->consensus_iupac() Function : Makes a consensus using IUPAC ambiguity codes from DNA and RNA. The output is in upper case except when gaps in a column force output to be in lower case. Note that if your alignment sequences contain a lot of IUPAC ambiquity codes you often have to manually set alphabet. Bio::PrimarySeq::_guess_type thinks they indicate a protein sequence. Returns : consensus string Argument : none Throws : on protein sequences

is_flush
Title : is_flush Usage : if( $ali->is_flush() ) : : Function : Tells you whether the alignment : is flush, ie all of the same length : : Returns : 1 or 0 Argument :

length
Title : length() Usage : $len = $ali->length() Function : Returns the maximum length of the alignment. To be sure the alignment is a block, use is_flush Returns : Argument :

maxdisplayname_length
Title : maxdisplayname_length Usage : $ali->maxdisplayname_length() Function : Gets the maximum length of the displayname in the alignment. Used in writing out various MSE formats. Returns : integer Argument :

no_residues
Title : no_residues Usage : $no = $ali->no_residues Function : number of residues in total in the alignment Returns : integer Argument :

no_sequences
Title : no_sequences Usage : $depth = $ali->no_sequences Function : number of sequence in the sequence alignment Returns : integer Argument : None

percentage_identity
Title : percentage_identity Usage : $id = $align->percentage_identity Function: The function calculates the percentage identity of the alignment Returns : The percentage identity of the alignment (as defined by the implementation) Argument: None

overall_percentage_identity
Title : percentage_identity Usage : $id = $align->percentage_identity Function: The function calculates the percentage identity of the conserved columns Returns : The percentage identity of the conserved columns Args : None

average_percentage_identity
Title : average_percentage_identity Usage : $id = $align->average_percentage_identity Function: The function uses a fast method to calculate the average percentage identity of the alignment Returns : The average percentage identity of the alignment Args : None Methods to map a sequence position into an alignment column and back. column_from_residue_number() does the former. The latter is really a property of the sequence object and can done using Bio::LocatableSeq::location_from_column: # select somehow a sequence from the alignment, e.g. my $seq = $aln->get_seq_by_pos(1); #$loc is undef or Bio::LocationI object my $loc = $seq->location_from_column(5);

column_from_residue_number
Title : column_from_residue_number Usage : $col = $ali->column_from_residue_number( $seqname, $resnumber) Function: This function gives the position in the alignment (i.e. column number) of the given residue number in the sequence with the given name. For example, for the alignment Seq1/91-97 AC..DEF.GH Seq2/24-30 ACGG.RTY.. Seq3/43-51 AC.DDEFGHI column_from_residue_number( "Seq1", 94 ) returns 5. column_from_residue_number( "Seq2", 25 ) returns 2. column_from_residue_number( "Seq3", 50 ) returns 9. An exception is thrown if the residue number would lie outside the length of the aligment (e.g. column_from_residue_number( "Seq2", 22 ) Note: If the the parent sequence is represented by more than one alignment sequence and the residue number is present in them, this method finds only the first one. Returns : A column number for the position in the alignment of the given residue in the given sequence (1 = first column) Args : A sequence id/name (not a name/start-end) A residue number in the whole sequence (not just that segment of it in the alignment) Methods to manipulate the display name. The default name based on the sequence id and subsequence positions can be overridden in various ways.

displayname
Title : displayname Usage : $myalign->displayname("Ig", "IgA") Function : Gets/sets the display name of a sequence in the alignment : Returns : A display name string Argument : name of the sequence displayname of the sequence (optional)

set_displayname_count
Title : set_displayname_count Usage : $ali->set_displayname_count Function : Sets the names to be name_# where # is the number of times this name has been used. Returns : None Argument : None

set_displayname_flat
Title : set_displayname_flat Usage : $ali->set_displayname_flat() Function : Makes all the sequences be displayed as just their name, not name/start-end Returns : 1 Argument : None

set_displayname_normal
Title : set_displayname_normal Usage : $ali->set_displayname_normal() Function : Makes all the sequences be displayed as name/start-end Returns : None Argument : None