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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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AUTHOR

Juguang Xiao <juguang@tll.org.sg>

NAME

Bio::EnsEMBL::Utils::CigarString, a utilites module to generate cigar strings

DESCRIPTION

Sequence alignment hits were previously stored within the core database as ungapped alignments. This imposed 2 major constraints on alignments:

a) alignments for a single hit record would require multiple rows in the database, and b) it was not possible to accurately retrieve the exact original alignment.

Therefore, in the new branch sequence alignments are now stored as ungapped alignments in the cigar line format (where CIGAR stands for Concise Idiosyncratic Gapped Alignment Report).

In the cigar line format alignments are stored as follows:

  M: Match
  D: Deletion
  I: Insertion

An example of an alignment for a hypthetical protein match is shown below:

  Query:   42 PGPAGLP----GSVGLQGPRGLRGPLP-GPLGPPL...
              PG    P    G     GP   R      PLGP
  Sbjct: 1672 PGTP*TPLVPLGPWVPLGPSSPR--LPSGPLGPTD...

This would be stored in the protein_align_feature table as the following cigar line:

  7M4D12M2I2MD7M

split_hsp

    Name  : split_hsp (this name is derived from the original sub in BlastWorn)
    Usage : my $hsp; # a ready Bio::Search::HSP::GenericHSP object.
my $factory = new Bio::EnsEMBL::Utils::CigarString;
my $cigar_string = $factory->split_hsp($hsp);
  
    Function: generate cigar string.
    Argument: a HSP object.
    Returns : a text string.
  

generate_cigar_string

  Name : generate_cigar_string
  Usage: $cigar_string = $self->generate_cigar_string(\@qchars, \@hchars);
  Function: generate the cigar string for a piece of alignment.
  Args:     2 array references. The lengths of 2 arrays are the same
  Return:   a cigar string

generate_cigar_string_by_hsp

  Name :    generate_cigar_string_by_hsp
  Usage :   my $hsp; # a ready GenericHSP object
my $cigar_string = $self->generate_cigar_string_by_hsp($hsp);
  Function: generate a cigar string by given HSP object.
  Args :    a GenericHSP object
  Returns:  a text string of cigar string