Genbank

nebgb is a Genbank file parser library. Usage: >>> import nebgb >>> rec = nebgb.parse_file("./test/data/simple-1.gb").next() >>> rec.locus["name"] 'NP_034640' >>> rec.locus["length"] 182 >>> rec.keywords["source"]["name"] 'house mouse' >>> rec.features[1]["properties"]["product"]... Platforms: *nix

Bio::Seq is a sequence object, with features. SYNOPSIS # This is the main sequence object in Bioperl # gets a sequence from a file $seqio = Bio::SeqIO->new( -format => embl , -file => myfile.dat); $seqobj = $seqio->next_seq(); # SeqIO can both read and write sequences; see Bio::SeqIO #... Platforms: *nix

Easyfig enables the creation of linear comparison figures showing BLAST matches between multiple genomic loci or prokaryote genomes. Easyfig has an easy-to-use graphical user interface and is able to launch BLAST searches interactively. Features: BLAST comparisons between multiple genomic regions... Platforms: Windows

Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format. A CGI-based web interface is also available. Please cite: Lee, W., Chen S.L. BioTechniques 33:1334-1341 (Dec 20 Platforms: Windows, Mac, Linux

ORFer reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. ORFprimer is an extended software package for high throughput PCR primer design for biological sequences Platforms: Windows, Mac, BSD, Solaris, Linux

Design primers based on length, melting temperature, GC content, hairpins, dimerization, nucleotide repeats, and 3' GC clamp criteria.Import data from files or from Genbank. Platforms: Matlab

GBParsy is a library of functions that parses the GenBank flatfile, which is a representative and popular sequence format. The library is optimized for speed and efficient use of memory so it can rapidly parse large sequence such as Arabidopsis chromosome for genomic analysis. GBParsyPy is... Platforms: Mac

Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, gapped... Platforms: Mac

BioFace is simple software for editing and analyzing DNA, RNA, and protein sequences that is written in Java using SWT and JFace as libraries. Opening GenBank, FASTA, EMBL, or simple sequence files and analizing these sequences can be done. Platforms: *nix

Bio::AnnotationCollectionI is a Perl interface for annotation collections. SYNOPSIS # get an AnnotationCollectionI somehow, eg $ac = $seq->annotation(); foreach $key ( $ac->get_all_annotation_keys() ) { @values = $ac->get_Annotations($key); foreach $value ( @values ) { # value is an... Platforms: *nix

Bio::Tools::CodonTable is a bioperl codon table object. SYNOPSIS # This is a read-only class for all known codon tables. The IDs are # the ones used by nucleotide sequence databases. All common IUPAC # ambiguity codes for DNA, RNA and animo acids are recognized. # to use use... Platforms: *nix

Bio::Graphics::Panel is a Perl module to generate GD images of Bio::Seq objects. SYNOPSIS # This script parses a GenBank or EMBL file named on the command # line and produces a PNG rendering of it. Call it like this: # render.pl my_file.embl | display - use strict; use Bio::Graphics;... Platforms: *nix

Bio::Network::IO::dip_tab is a Perl class for parsing interaction data in DIP tab-delimited format. SYNOPSIS Do not use this module directly, use Bio::Network::IO. For example: my $io = Bio::Network::IO->new(-format => dip_tab, -file => data.dip); my $network = $io->next_network; The... Platforms: *nix

biOpen is a new and unique DNA and protein sequence analysis and structure visualization software based on dynamic integration of analysis tools. This evaluation version includes the interactive multiple trace view, the Documentation window, DNA/RNA analysis tools (including Contig Assembly),... Platforms: Mac

CLC Free Workbench is the foundation for all bioinformatics workbenches from CLC bio. This software package is a community edition, available for download free of charge.The workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management,... Platforms: Mac

MacVector... Researchers who want a simple but comprehensive desktop sequence analysis application continually turn to MacVector, the leading sequence analysis package for the Macintosh. MacVector provides sequence editing, primer design, Internet database searches, protein analysis, sequence... Platforms: Mac

CLC DNA Workbench (formerly known as CLC Gene Workbench) creates a software environment enabling users to make a large number of advanced DNA sequence analyses, combined with smooth data management, and excellent graphical viewing and output options.We invite you to try a fully functional demo of... Platforms: Mac

Sequencher is the industry standard software for DNA sequence analysis. It works with all automated sequencers and is widely known for its lightning-fast contig assembly, short learning curve, user-friendly editing tools, and superb technical support. First released almost 15 years ago,... Platforms: Mac

XPlasMap... Draw plasmid & genomic DNA maps showing restriction sites, genes, multiple cloning sites, and other features; copy and paste between maps; import from GenBank files; save as JPG or PNG Platforms: Mac

Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis,... Platforms: Windows