Documentation

  • bp_aacomp - amino acid composition of protein sequences
  • bp_bioflat_index.pl - index sequence files using Bio::DB::Flat
  • bp_biogetseq - sequence retrieval using OBDA registry
  • bp_chaos_plot - a chaos plot from DNA and RNA sequences
  • bp_dbsplit - script to split an input set of database(s) into smaller pieces
  • bp_extract_feature_seq - extract the corresponding sequence for a specified feature type
  • fastm9_to_table - turn FASTA -m 9 output into NCBI -m 9 tabular output
  • bp_fetch.pl - fetches sequences from bioperl indexed databases
  • bp_filter_search - filters searchio results, outputting a tab delimited summary
  • bp_find-blast-matches.pl - extract DNA sequences based on BLAST hits
  • bp_gccalc - GC content of nucleotide sequences
  • bp_genbank2gff3.pl - Genbank-gtgbrowse-friendly GFF3
  • bp_index.pl - indexes files for use by bp_fetch.pl
  • bp_local_taxonomydb_query - query a local TaxonomyDB for species or taxonid
  • bp_make_mrna_protein - Convert an input mRNA/cDNA sequence into protein
  • bp_mask_by_search - mask sequence(s) based on its alignment results
  • bp_mrtrans - implement a transformer of alignments from protein to mrna coordinates
  • bp_mutate.pl - randomly mutagenize a single protein or DNA sequence
  • bp_nexus2nh - convert nexus format trees (from PAUP* and MrBayes) to new hampshire
  • bp_nrdb.PLS - a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
  • bp_oligo_count - oligo count and frequency
  • bp_process_gadfly.pl - Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
  • bp_process_sgd.pl - Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
  • bp_revtrans-motif - Reverse translate a Profam-like protein motif
  • bp_search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks
  • bp_search2gff - turn a SearchIO report into GFF
  • bp_search2table - turn SearchIO parseable reports into tab delimited format like NCBI's -m 9
  • bp_search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix
  • bp_seq_length.pl - lists the number of bases and number of sequences in specified sequence database files
  • bp_seqconvert - generic BioPerl sequence format converter
  • bp_seqcut.pl - cut FASTA sequences with a given range
  • bp_seqpart.pl - Takes one or more sequence files and splits them into a number of load balanced files.
  • bp_seqret - bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
  • bp_seqretsplit - split a sequence (or stream) into a single file per sequence
  • bp_split_seq - splits a sequence into equal sized chunks with an optional overlapping range
  • bpsreformat - convert sequence formats
  • bp_taxid4species - simple script which returns the NCBI Taxonomic id for a requested species
  • bp_taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of species names
  • bp_translate_seq - translates a sequence
  • bp_tree2pag - convert Bio::TreeIO parseable format trees to pagel format
  • bp_unflatten_seq - unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy

Modules

Provides