Free ncbi software for linux

ToBiX is a Morphix-based Linux live CD containing a range of specialist applications for bioinformatics. With this distrubution you just boot from the CD and you have a fully functional LINUX OS distribution with open source applications.
Besides using some RAM, ToBiX doesnt touch the host computer and is ideal for presentations, workshops or other learning or scientific activity on bioinformatics and computational biology.
ToBiX comprises some of the most useful and powerful bioinformatics tools such as:
- Blast 2.0 - Basic Local Alignment Search Tool for rapid searching of nucleotide and protein databases;
- Copasi - software application for simulation and analysis of biochemical networks;
- mpiBLAST - MPI based parallel implementation of NCBI BLAST;
- SimWiz - collection of Java tools for visualization of data resulting from different kinds of biochemical simulation processes;
- Cellware - tool to model whole cell biochemical reactions;
- Gromacs - molecular dynamics simulation package;
- SBML-Editor - tool for the quick creation and edition of SBML files;
- Stocks 2 - software for simulation of biochemical processes using Maximal Time Step Method

Bio::GMOD is a unified API for Model Organism Databases.

SYNOPSIS

Check the installed version of a MOD
use Bio::GMOD::Util::CheckVersions.pm
my $mod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase);
my $version = $mod->live_version;
Update a MOD installation
use Bio::GMOD::Update;
my $mod = Bio::GMOD::Update->new(-mod=>WormBase);
$gmod->update();
Fetch a list of genes from a MOD
use Bio::GMOD::Query;
my $mod = Bio::GMOD::Query->new(-mod=>WormBase);
my @genes = $mod->fetch(-class=>Gene,-name=>unc-26);

Bio::GMOD is a unified API for accessing various Model Organism Databases. It is a part of the Generic Model Organism Database project, as well as distributed on CPAN.

MODs are highly curated resources of biological data. Although they typically incorporate sequence data housed at community repositories such as NCBI, they place this information within a framework of biological fuction gelaned from the published literature of experiments in model organisms.

Given the great proliferation of MODs, cross-site data mining strategies have been difficult to implement. Such strategies typically require a familiarity with both the underlying data model and the historical vocabulary of the model system.

Furthermore, the quickly-evolving nature of these projects have made installing a MOD locally and keeping it up-to-date a delicate and time-consuming experience.

Sequence Analysis project is a collage of coding projects which I have written over the past several years for various clients in my work as a bioinformatics consultant.

These clients have graciously allowed me to release these works into the public domain as freeware for Macintosh OS X in order to promote the platform and to encourage migration from Classic.

The upper window panel can hold several sequences, which are both editable and selectable. The tabs in the lower analysis panel try to keep up with the current sequence selection to provide immediate feedback. The selection is used in some modules as only the portion being analyzed for other modules i.e. Digest is used to determine if enzymes cut in the in or outside of the selection.

Most commonly available sequence formats have been reverse engineered. You can also access a sequences from the NCBI via its GID or UID. This currently cannot be done from behind a firewall.

Most of the analyses are simple enough that they are obvious to use, Composition, pI. Others could stand some documenation i.e. Pairwise and Primer Design. The Publish tab uses a string to control the layout. Click on the Legend button for some help.

BioBrew Linux is an open source Linux distribution that is enhanced for life scientists. It is customized for cluster and bioinformatics computing. It automates cluster installation, includes all the HPC software a cluster enthusiast needs, and contains popular bioinformatics applications.

BioBrew Linux is an open source Linux distribution based on the NPACI Rocks cluster software and enhanced for bioinformaticists and life scientists. While it looks, feels, and operates like ordinary Red Hat Linux, BioBrew Linux includes popular cluster software e.g. MPICH, LAM-MPI, PVM, Modules, PVFS, Myrinet GM, Sun Grid Engine, gcc, Ganglia, and Globus, *and* popular bioinformatics software e.g. the NCBI toolkit, BLAST, mpiBLAST, HMMER, ClustalW, GROMACS, PHYLIP, WISE, FASTA, and EMBOSS.

It runs on everything from notebook computers to large clusters. BioBrew Linux for the Itanium architecture is only available for purchase at this time through Callident. Please contact Brewmeister Glen Otero for information regarding BioBrew Linux on Itanium.

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 Bio::Tools::CodonTable;

# defaults to ID 1 "Standard"
$myCodonTable = Bio::Tools::CodonTable->new();
$myCodonTable2 = Bio::Tools::CodonTable -> new ( -id => 3 );

# change codon table
$myCodonTable->id(5);

# examine codon table
print join ( , "The name of the codon table no.", $myCodonTable->id(4),
"is:", $myCodonTable->name(), "n");

# translate a codon
$aa = $myCodonTable->translate(ACU);
$aa = $myCodonTable->translate(act);
$aa = $myCodonTable->translate(ytr);

# reverse translate an amino acid
@codons = $myCodonTable->revtranslate(A);
@codons = $myCodonTable->revtranslate(Ser);
@codons = $myCodonTable->revtranslate(Glx);
@codons = $myCodonTable->revtranslate(cYS, rna);

#boolean tests
print "Is a startn" if $myCodonTable->is_start_codon(ATG);
print "Is a termianatorn" if $myCodonTable->is_ter_codon(tar);
print "Is a unknownn" if $myCodonTable->is_unknown_codon(JTG);

Codon tables are also called translation tables or genetics codes since that is what they try to represent. A bit more complete picture of the full complexity of codon usage in various taxonomic groups presented at the NCBI Genetic Codes Home page.

CodonTable is a BioPerl class that knows all current translation tables that are used by primary nucleotide sequence databases (GenBank, EMBL and DDBJ). It provides methods to output information about tables and relationships between codons and amino acids.

This class and its methods recognized all common IUPAC ambiguity codes for DNA, RNA and animo acids. The translation method follows the conventions in EMBL and TREMBL databases.
It is a nuisance to separate RNA and cDNA representations of nucleic acid transcripts. The CodonTable object accepts codons of both type as input and allows the user to set the mode for output when reverse translating. Its default for output is DNA.

Note: This class deals primarily with individual codons and amino acids. However in the interest of speed you can translate longer sequence, too. The full complexity of protein translation is tackled by Bio::PrimarySeqI::translate.

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed protein families.
SYNOPSIS
use Bio::Tools::Run::TribeMCL;
use Bio::SearchIO;
# 3 methods to input the blast results
# straight forward raw blast output (NCBI or WU-BLAST)
my @params = (inputtype=>blastfile);
# OR
# markov program format
# protein_id1 protein_id2 evalue_magnitude evalue_factor
# for example:
# proteins ENSP00000257547 and ENSP00000261659
# with a blast score evalue of 1e-50
# and proteins O42187 and ENSP00000257547
# with a blast score evalue of 1e-119
# entry would be
my @array = [[qw(ENSP00000257547 ENSP00000261659 1 50)],
[qw(O42187 ENSP00000257547 1 119)]];
my @params = (pairs=>@array,I=>2.0);
# OR
# pass in a searchio object
# slowest of the 3 methods as it does more rigourous parsing
# than required for us here
my $sio = Bio::SearchIO->new(-format=>blast,
-file=>blast.out);
my @params=(inputtype=>searchio,I=>2.0);
# you can specify the path to the executable manually in the following way
my @params=(inputtype=>blastfile,I=>2.0,
mcl=>/home/shawn/software/mcl-02-150/src/shmcl/mcl,
matrix=>/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix);
my $fact = Bio::Tools::Run::TribeMCL->new(@params);
# OR
$fact->matrix_executable(/home/shawn/software/mcl-02-150/src/contrib/tribe/tribe-matrix);
$fact->mcl_executable(/home/shawn/software/mcl-02-150/src/shmcl/mcl);
# to run
my $fact = Bio::Tools::Run::TribeMCL->new(@params);
# Run the program
# returns an array reference to clusters where members are the ids
# for example :2 clusters with 3 members per cluster:
# $fam = [ [mem1 mem2 mem3],[mem1 mem2 mem3]]
# pass in either the blastfile path/searchio obj/the array ref to scores
my $fam = $fact->run($sio);
# print out your clusters
for (my $i = 0; $i
print "Cluster $i t ".scalar(@{$fam->[$i]})." membersn";
foreach my $member (@{$fam->[$i]}){
print "t$membern";
}
}
This clustering is achieved by analysing similarity patterns between proteins in a given dataset, and using these patterns to assign proteins into related groups. In many cases, proteins in the same protein family will have similar functional properties.
Enhancements:
- Perl

Genomorama: Genome Visualization is a multi-scale, multi-genome, multi-platform visualization and analysis program. It provides a powerful yet easy to use interface that leverages the visualization power of modern computers (via OpenGL) and the substantial bioinformatic infrastructure provided by the NCBI (via the NCBI C toolkit).
Genomorama is written in portable, highly optimized C++ and comes in three "flavors" that allow it to run natively on (most) modern operating systems: OS X (using Carbon), Microsoft Windows (using MFC), and Linux (using Motif). Executables and source code are freely provided for all flavors.
Main features:
- High performance has not been sacrificed on the altar of portability
- OpenGL graphics take advantage of the video-game optimized graphics cards available in most desktop and laptop computers.
- C++ allows transparent and complete utilization of system resources (like memory).
- Native windowing toolkits (Carbon, MFC and Motif) for every operating system facilitate responsiveness and ease of use.
- A stand-alone, self-contained executable frees Genomorama from dependence on third party applications.
- Source code for all platforms is freely available.
- An attractive, full featured user interface
- Genomorama presents a clean, uncluttered user interface.
- Multi-scale rendering displays relevant details while maintaining readability.
- Use a keyboard or a mouse to efficiently zoom, pan and explore genomes of arbitrary size.
- Attractive WYSIWYG Postscript and GIF output formats yield publication quality images.
- Novel features to aid genome analysis
- In addition to the standard searching options (like query by sequence and gene name), Genomorama offers "forward and reverse" DNA hybridization based searches.
- Provide a pair of PCR primers, and Genomorama will output the amplicons.
- Provide a hybridization probe and Genomorama will find binding sites.
- Provide a pair of Padlock probes and Genomorama will identify binding locations
- Provide a set of PCR primer criteria (length, melting temperature, base composition, etc.) and Genomorama will find PCR primers.
- Genomorama can display and search an arbitrary number of genomes (limited only by computer memory).
- Harness the power of the NCBI toolkit to directly access and search the NCBI Entrez database.
- Compute melting profile, in addition to traditional base composition plots (i.e. %G+C, %A+T, etc).
Enhancements:
- This release fixes the following bugs: parsing gbk files that contain single base annotations on the complement strand;
- missed exact matches at 3 end of target sequence;
- fragile parsing of annotation range;
- downloading of very large Genbank records (i.e. human chromosomes);
- and omitted intergenic space following single base annotations (i.e. SNPs).
- Custom color records are now saved to and read from GBK files.
- An OS X Intel-specific executable has been added.
- The information dialog box has been made resizable.

PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. PerlPrimer aims to automate and simplify the process of primer design.
Main features:
- Calculation of possible primer-dimers
- Retrieval of genomic or cdna sequences from Ensembl (including both sequences automatically for QPCR)
- Ability to BLAST search primers using the NCBI server or a local server
- Results can be saved or optionally exported in a tab-delimited format that is compatible with most spreadsheet applications.
- ORF and CpG island detection algorithms
- Ability to add cloning sequences to primers, automatically adjusted to be in-frame
- QPCR primer design without manual intron-exon boundary entry
PerlPrimer calculates primer melting temperature using J. SantaLucias extensive nearest-neighbour thermodynamic parameters. To adjust for the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+, dNTPs and primers, or use standard PCR conditions. The result is a highly accurate prediction of primer melting temperature, giving rise to a maximum yeild of product when amplified.
PerlPrimer is written in Perl and Perl/Tk. In addition, for QPCR functionality PerlPrimer uses the open-source Spidey executable from NCBI, and restriction enzyme data from the REBASE project is used when adding cloning sites. The program is designed to be cross-platform compatible and has been developed and tested on both Microsoft Windows and GNU/Linux-based operating systems. Users have also reported success using the program under Mac OS X.
Enhancements:
- Ensembl compatibility restored once again (slight change in the searchview output was causing problems)