.\" Automatically generated by Pod::Man 4.10 (Pod::Simple 3.35) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' . ds C` . ds C' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is >0, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. Of course, you'll have to process the .\" output yourself in some meaningful fashion. .\" .\" Avoid warning from groff about undefined register 'F'. .de IX .. .nr rF 0 .if \n(.g .if rF .nr rF 1 .if (\n(rF:(\n(.g==0)) \{\ . if \nF \{\ . de IX . tm Index:\\$1\t\\n%\t"\\$2" .. . if !\nF==2 \{\ . nr % 0 . nr F 2 . \} . \} .\} .rr rF .\" ======================================================================== .\" .IX Title "TFBS::Matrix::Alignment 3pm" .TH TFBS::Matrix::Alignment 3pm "2018-11-02" "perl v5.28.0" "User Contributed Perl Documentation" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" TFBS::Matrix::Alignment \- class for alignment of PFM objects .SH "SYNOPSIS" .IX Header "SYNOPSIS" .IP "\(bu" 1 Making an alignment: (See documentation of individual TFBS::DB::* modules to learn how to connect to different types of pattern databases and retrieve TFBS::Matrix::* objects from them.) .Sp .Vb 5 \& my $db_obj = TFBS::DB::JASPAR2\->new \& (\-connect => ["dbi:mysql:JASPAR2:myhost", \& "myusername", "mypassword"]); \& my $pfm1 = $db_obj\->get_Matrix_by_ID("M0001", "PFM"); \& my $pfm2 = $db_obj\->get_Matrix_by_ID("M0002", "PFM"); \& \& my $alignment= new TFBS::Matrix::Alignment( \& \-pfm1=>$pfm1, \& \-pfm2=>$pfm2, \& \-binary=>"/TFBS/Ext/matrix_aligner", \& ); .Ve .SH "DESCRIPTION" .IX Header "DESCRIPTION" TFBS::Matrix::Alignment is a class for representing and performing pairwise alignments of profiles (in the form of \s-1TFBS::PFM\s0 objects) Alignments are preformed using a semi-global variant of the Needleman-Wunsch algorithm that only permits the opening of one internal gap. Fore reference, the algorithm is described in Sandelin et al Funct Integr Genomics. 2003 Jun 25 .SH "FEEDBACK" .IX Header "FEEDBACK" Please send bug reports and other comments to the author. .SH "AUTHOR \- Boris Lenhard" .IX Header "AUTHOR - Boris Lenhard" Boris Lenhard .SH "APPENDIX" .IX Header "APPENDIX" The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore. .SS "new" .IX Subsection "new" .Vb 5 \& Title : new \& Usage : my $alignment = TFBS::Matrix::Alignment\->new(%args) \& Function: constructor for the TFBS::Matrix::Alignment object \& Returns : a new TFBS::Matrix::Alignment object \& Args : # you must specify: \& \& \-pfm1, # a TFBS::Matrix::PFM object \& \-pfm2, # another TFBS::Matrix::PFM object \& \-binary, # a valid path to the comparison algorithm (matrixalign) \& \& \& ####### \& \& \-ext_penalty #OPTIONAL gap extension penalty in Needleman\-Wunsch \& algorithmstring. Default 0.01 \& \-open_penalty, #OPTIONAL gap opening penalty in Needleman\-Wunsch \& algorithmstring. Default 3.0 .Ve .SS "score" .IX Subsection "score" .Vb 5 \& Title : score \& Usage : my $score = $alignmentobject\->score(); \& Function: access an alignment score (where each aligned position can contribute max 2) \& Returns : a floating point number \& Args : none .Ve .SS "score" .IX Subsection "score" .Vb 5 \& Title : gaps \& Usage : my $nr_of_gaps = $alignmentobject\->gaps(); \& Function: access the number of gaps in an alignment \& Returns : an integer \& Args : none .Ve .SS "length" .IX Subsection "length" .Vb 5 \& Title : length \& Usage : my $length = $alignmentobject\->length(); \& Function: access the length of an alignment (ie thenumber of aligned positions) \& Returns : an integer \& Args : none .Ve .SS "strand" .IX Subsection "strand" .Vb 7 \& Title : strand \& Usage : my $strand = $alignmentobject\->strand(); \& Function: access the oriantation of the aligned patterns: \& ++= oriented as input \& +\-= second pattern is reverse\-complemented \& Returns : a string \& Args : none .Ve .SS "alignment" .IX Subsection "alignment" .Vb 7 \& Title : alignment \& Usage : my $alignment_string = $alignmentobject\->alignment(); \& Function: access a string describing the alignment \& Returns : an string, where each number refers to a position in respective PFM. \& Position numbering is according to orientation: ie if the second profile is \& reversed, position 1 corresponds to the last position in the input profile. \& Gaps are denoted as \- . \& \& RXR\-VDR \- 1 2 3 \- 4 5 \- \& PPARgamma\-RXRal 1 2 3 4 5 6 7 8 \& \& \& Args : none .Ve .SH "POD ERRORS" .IX Header "POD ERRORS" Hey! \fBThe above document had some coding errors, which are explained below:\fR .IP "Around line 39:" 4 .IX Item "Around line 39:" You forgot a '=back' before '=head1'