Weigel::Search

Weigel-Search is a collection of Perl modules for searching in FASTA-files.

Main Features:

• Different backends available. Currently Vmatch, Hypa and Agrep are supported. You can easily add own backends (important: choose the module for the Hypa backend as template).

• Approximate matches: You can define how many mismatches should be allowed (hamming distance). Vmatch and Agrep allow edit distances, in Hypa you can define the number of deletions and insertions.
• Generate databases (Hypa, Vmatch: calculate the suffix arrays).
• Alignment query-match as Bioperl Bio::SimpleAlign object.
• Displaying upstream and downstream regions of a match (only Hypa and Vmatch).
• Wobble pairs. Count GU mismatches as 0, 0.5 or 1 mismatch (Hypa).
• Nucleotide and protein databases
• Filter search results. You can write filters that define if a query-match pair should pass this filter (only Hypa and Vmatch).

Usage Example:

 use Weigel::Search;

 # construct a search object, use the Hypa backend. Other
 # backends are Vmatch and Agrep
 my $search_obj = Weigel::Search->new('Hypa');
 # $sbe is now a reference to the backend
 my $sbe = $search_obj->backend;
 # define a data directory (we put the suffix arrays there. 
 # you will probably need a lot of free disc space)
 $sbe->settings->datapath('data');
 mkdir($sbe->settings->datapath);
 # generate a suffix array. you have to do this only once.
 $sbe->generate_database_out_of_fastafile('Test.fasta', 'Description for the test Fastafile');
 # use this database for the next search 
 $sbe->settings->database('Test.fasta');
 # search for the reverse complement and allow 2 mismatches
 $sbe->settings->query('UGAACAGAAAG');
 $sbe->settings->reverse_complement(1);
 $sbe->settings->mismatches(2);
 $sbe->search();
 # output the alignments
 foreach my $res (@{$sbe->results}) {
    print $res->sequence->id . "\n";
    print $res->mark_subject_uppercase() . "\n";
    print $res->alignment_string() . "\n\n";
 }

See perldoc for more examples.

Weigel::RNA

This module filters putative MicroRNA targets in Weigel::Search search results. A mfold perl frontend is part of this package. It is very easy to use.

Main Features:

• MicroRNA target filter
• RNAcofold and mfold perl modules
• MicroRNA Designer modules (including powerful database modules that allow multiple designer clients)

Usage example:

 $sbe->settings->mismatches(5);

 # filter search results
 my $filter = Weigel::Search::Filter::MIRNAFilter->new();
 # don't delete results, only add a message if filter passed or not
 $filter->delete(0);
 # you can write own filters and apply all of them!
 my @filters = ( $filter );
 $sbe->settings->filters( @filters );
 $sbe->search();

Downloads:

Weigel::Search 0.12 (06/02/25)

Weigel::RNA soon!