NAME
Bioscripts
SYNOPSIS
A list of the scripts in Bioperl
DESCRIPTION
These scripts have been contributed by the developers and users of Bioperl. They are organized into directories roughly mirroring those in the Bioperl Bio directory. Please contact bioperl-l@bioperl.org if you are interested in contributing your own script.
scripts/align/align_on_codons.pl
Aligns nucleotide sequences based on codons in a specified reading frame.
scripts/align/aligntutorial.pl
Examples using EMBOSS, pSW, Clustalw, TCoffee, and Blast to align sequences.
scripts/align/clustalw.pl
A demonstration of the various uses of Alignment::Clustalw. See Bio::Tools::Run::Alignment::Clustalw for more.
scripts/align/simplealign.pl
A script that demonstrates some uses of AlignIO. Please see Bio::AlignIO for more information.
scripts/biblio/biblio.pl
A script that shows how to query bibliographic databases, such as Medline, using ids, keywords, and other fields. See Bio::Biblio for details.
scripts/biblio/biblio_soap.pl
Connect to and test a SOAP server using a Bio::Biblio object.
scripts/bioperl.pl
A Bioperl shell!
scripts/cluster/dbsnp.pl
How to parse a dbsnp XML file. See Bio::ClusterIO for details.
scripts/contributed/nmrpdb_parse.pl
Extracts individual conformers from an NMR-derived PDB file.
scripts/contributed/prosite2perl.pl
Convert Prosite motifs to Perl regular expressions.
scripts/contributed/rebase2list.pl
Script to convert rebase file to format compatible with Bio::Tools::RestrictionEnzyme.
scripts/das/das_server.pl
Sets up a minimal DAS annotation server, requires Apache::DBI and Bio::DB::GFF. See Bio::DB::GFF for details.
scripts/db/dbfetch
Creates a Web page to query a local SRS server and fetch sequences.
scripts/db/est_tissue_query.pl
Fetch EST sequences from local files or Genbank filtered by tissue using Bio::DB* or Bio::Index*.
scripts/db/flanks.pl
Fetch a sequence, find the sequences flanking a variant or SNP in the sequence given its position.
scripts/db/gb2features.pl
Shows how to extract all the features from a Genbank file. See Bio::Seq for more information on features.
scripts/db/getGenBank.pl
Retrieving Genbank entries over the Web using DB::GenBank. See Bio::DB::GenBank for more information.
scripts/db/get_seqs.pl
Fetches and formats sequences from GenBank, EMBL, or SwissProt over the network using Bio::DB*.
scripts/db/gff/*
Scripts that reformat sequence to GFF and load GFF format files into an indexed database - see Bio::DB::GFF for more information.
scripts/db/rfetch.pl
A script that uses Bio::DB::Registry to retrieve sequences from EMBL, reformat them, and print them. See Bio::DB::Registry.
scripts/db/use_registry.pl
Script that shows how to use Bio::DB::Registry, part of Bioperl's integration with OBDA, the Open Bio Database Access registry scheme. See Bio::DB::Registry for more information.
scripts/exceptions/*
Scripts that demonstrate how to throw and catch Error.pm objects.
scripts/generate_random_seq.pl
Writes random RNA, DNA, or protein sequence of given length.
scripts/graphics/feature_draw.pl
Script that accepts files in GFF or tab-delimited format and creates corresponding PNG image files. See Bio::Graphics and Bio::Graphics::FeatureFile for more information.
scripts/graphics/render_sequence.pl
This scripts fetchs a sequence from a remote database, extracts its features (CDS, gene, tRNA), and creates a graphic representation of the sequence in PNG or GIF format. See Bio::DB::BioFetch and Bio::Graphics.
scripts/index/bpfetch.pl
Fetch sequences from local indexed database or over the network and reformat using Bio::Index* and Bio::DB*.
scripts/index/bpindex.pl
Indexes local databases, partners with bpfetch.pl.
scripts/liveseq/change_gene.pl
A script showing how to use LiveSeq::Mutator and LiveSeq::Mutation. Please see Bio::LiveSeq::Mutator and Bio::LiveSeq::Mutation for more information.
scripts/longorf.pl
A script that finds the longest ORF in one or more nucleotide sequences.
scripts/make_mrna_protein.pl
Translate a cDNA or ORF to protein using Bio::Seq's translate() method.
scripts/make_primers.pl
Design PCR primers given a sequence and the positions of the start and stop codons in the sequence's ORF.
scripts/rev_and_trans.pl
Examples using Bio::Seq.pm for reversing and translating sequences. See Bio::Seq for more information.
scripts/revcom_dir.pl
Eeturn reverse complement sequences of all sequences in the current directory and save them in the same directory.
scripts/root_object/*
Scripts that demonstrate uses of the Bio::Root modules.
scripts/root_object/vector/vector.pl
Script to test Bio::Root::Vector.
scripts/searchio/*
A number of scripts illustrating the use of Bio::SearchIO for parsing Blast and PSI-Blast results. See Bio::SearchIO for more information.
scripts/searchio/waba2gff.pl
Convert raw WABA output to one type of GFF.
scripts/seq/*
Example code for working with multiple sequence files, including formatting, printing, and filtering based on length or description or ID.
scripts/seqstats/aacomp.pl
Calculate amino acid composition of a protein using Tools::CodonTable and Tools::IUPAC. See Bio::Tools::IUPAC and Bio::Tools::CodonTable for more information.
scripts/seqstats/chaos_plot.pl
Produce a PNG or JPEG chaos plot given a DNA sequence using GD.pm.
scripts/seqstats/gccalc.pl
Calculate %GC given a DNA sequence using Tools::SeqStats. See Bio::Tools::SeqStats for more information.
scripts/seqstats/oligo_count.pl
Calculates oligomer frequencies given an oligomer length and a sequence.
scripts/structure/struct_example*
Scripts that show how to examine details of the 3D structure of a protein by parsing a PDB file. See Bio::Structure::IO for more information.
scripts/subsequence.cgi
CGI script to fetch a sequence from Genbank and extract a subsequence using DB::GenBank. See Bio::DB::GenBank.
scripts/tk/gsequence
Create a Protein Sequence Control Panel GUI with Gtk.
scripts/tk/hitdisplay.pl
Create a GUI for displaying Blast results using Tk::HitDisplay. Please see Bio::Tk::HitDisplay for more information.
scripts/tools/gb_to_gff.pl
Extracts top-level sequence features from Genbank-formatted sequence files using Tools::GFF. See Bio::Tools::GFF.
scripts/tools/gff2ps.pl
Takes an input file in GFF format and draws its genes and features as Postscript using Tools::GFF. See Bio::Tools::GFF.
scripts/tools/parse_codeml.pl
Script that parses output from codeml, one of the PAML programs. See Bio::Tools::Phylo::PAML.
scripts/tools/psw.pl
Example code for using the XS extensions for comparing proteins using Smith-Waterman.
scripts/tools/remote_blast.pl
This script executes remote Blast using RemoteBlast. See Bio::Tools::Run::RemoteBlast for more information.
scripts/tools/restriction.pl
Example code for using the RestrictionEnzyme module. See Bio::Tools::RestrictionEnzyme for more information.
scripts/tools/run_genscan.pl
Run GENSCAN on multiple sequences and create output sequence files using Tools::Genscan. Please see Bio::Tools::Genscan for more information.
scripts/tools/seq_pattern.pl
A script that shows how to use sequences as regular expressions using Tools::SeqPattern. Please see Bio::Tools::SeqPattern for more information.
scripts/tools/state-machine.pl
A demonstration of how to create a state machine using StateMachine::AbstractStateMachine. Please see Bio::Tools::StateMachine::AbstractStateMachine for more information.
scripts/tools/test-genscan.pl
Script for testing and demonstrating Bio::Tools::Genscan.
scripts/tree/paup2phylip.pl
Convert a PAUP tree block to Phylip format.