📦 bioperl

B

• bp_aacomp(1p)amino acid composition of protein sequences✨
• bp_bioflat_index(1p)index sequence files using Bio::DB::Flat✨
• bp_biogetseq(1p)sequence retrieval using OBDA registry✨
• bp_dbsplit(1p)script to split an input set of database(s) into smaller pieces✨
• bp_extract_feature_seq(1p)extract the corresponding sequence for a specified feature type✨
• bp_fastam9_to_table(1p)turn FASTA -m 9 output into NCBI -m 9 tabular output✨
• bp_fetch(1p)fetches sequences from bioperl indexed databases✨
• bp_filter_search(1p)filters searchio results, outputting a tab delimited summary✨
• bp_find-blast-matches(1p)extract DNA sequences based on BLAST hits✨
• bp_gccalc(1p)GC content of nucleotide sequences✨
• bp_genbank2gff3(1p)Genbank->gbrowse-friendly GFF3✨
• bp_index(1p)indexes files for use by bp_fetch.pl✨
• bp_local_taxonomydb_query(1p)query a local TaxonomyDB for species or taxonid✨
• bp_make_mrna_protein(1p)Convert an input mRNA/cDNA sequence into protein✨
• bp_mask_by_search(1p)mask sequence(s) based on its alignment results✨
• bp_mrtrans(1p)implement a transformer of alignments from protein to mrna coordinates✨
• bp_mutate(1p)randomly mutagenize a single protein or DNA sequence✨
• bp_nexus2nh(1p)convert nexus format trees (from PAUP* and MrBayes) to new hampshire✨
• bp_nrdb(1p)a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases✨
• bp_oligo_count(1p)oligo count and frequency✨
• bp_process_gadfly(1p)Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser✨
• bp_process_sgd(1p)Massage SGD annotation flat files into a version suitable for the Generic Genome Browser✨
• bp_revtrans-motif(1p)Reverse translate a Profam-like protein motif✨
• bp_search2alnblocks(1p)Turn SearchIO parseable reports(s) into a set of aligned blocks✨
• bp_search2gff(1p)turn a SearchIO report into GFF✨
• bp_search2table(1p)turn SearchIO parseable reports into tab delimited format like NCBI's -m 9✨
• bp_search2tribe(1p)Turn SearchIO parseable reports(s) into TRIBE matrix✨
• bp_seq_length(1p)lists the number of bases and number of sequences in specified sequence database files✨
• bp_seqconvert(1p)generic BioPerl sequence format converter✨
• bp_seqcut(1p)cut FASTA sequences with a given range✨
• bp_seqpart(1p)Takes one or more sequence files and splits them into a number of load balanced files.✨
• bp_seqret(1p)bioperl implementation of sequence fetch from local db (like EMBOSS seqret)✨
• bp_seqretsplit(1p)split a sequence (or stream) into a single file per sequence✨
• bp_split_seq(1p)splits a sequence into equal sized chunks with an optional overlapping range✨
• bp_sreformat(1p)convert sequence formats✨
• bp_taxid4species(1p)simple script which returns the NCBI Taxonomic id for a requested species✨
• bp_taxonomy2tree(1p)Building a taxonomic tree based on the full lineages of a set of species names✨
• bp_translate_seq(1p)translates a sequence✨
• bp_tree2pag(1p)convert Bio::TreeIO parseable format trees to pagel format✨
• bp_unflatten_seq(1p)unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy✨