Genome
Timina is a Java web-based application for automation of all steps of a genome sequencing project: submission, assembly and annotation of sequences.
Platforms: Mac, BSD, Linux
License: Freeware | Size: 8.24 MB | Download (43): Timina Download |
WGAViewer is a suite of JAVA software tools that provides a user-friendly interface to annotate, visualize, and help interpret the full set of P values emerging from a whole genome association (WGA) study.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 666.49 KB | Download (50): WGAViewer Download |
dbSNPtool starts a GUI to return polymorphism data from dbSNPwww.ncbi.nih.gov/SNP Calling dbsnptool start the GUI, SNP % records are returned based on keyword. Each result is presented in a % listbox, clicking on the entry loads the sequence into the sequence %viewer. Information is presenting...
Platforms: Matlab
License: Freeware | Size: 40.96 KB | Download (43): dbSNP tool Download |
MCGH is a Matlab toolbox with graphical interface to analysis DNA microarray-based comparative genomic hybridization (CGH) experiments. CGH on DNA microarray enable us to measure the copy numbers of thousands of genes through the genome. M-CGH allows us to visualize the copy number changes...
Platforms: Matlab
License: Freeware | Size: 5.18 MB | Download (41): MCGH Download |
GETHGVBASE returns polymorphism data from the human genome variation db http://hgvbase.cgb.ki.seHGVDATA = gethgvbase(SNPID) reads in a %hgvbase web record fromEMBL and creates a structure DATA %containing fields correspondingto the hgvBase keywords.FIELDNAME DESCRIPTIONS: a complete %description...
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (43): gethgvbase Download |
The BLAST Ring Image Generator (BRIG) is a cross-platform JAVA application, it has a graphical user interface, which takes the user step-by-step through the configuration of a genome circular visualization.
Platforms: Mac
License: Freeware | Size: 12.8 MB | Download (56): BLAST Ring Image Generator Download |
The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap-closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the...
Platforms: Mac
License: Freeware | Size: 2.62 MB | Download (35): OSLay Download |
bedtools: a flexible suite of utilities for comparing genomic features. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM....
Platforms: Mac
License: Freeware | Size: 890.88 KB | Download (38): BEDTools Download |
JDSA is a Java program that will degenerately search DNA sequences. This program searches sequences for multiple nucleotides at a given position (positional degeneracy), limited overall sequence accuracy (group degeneracy) or variable spacing between multiple DNA sequences (spacing degeneracy)....
Platforms: Mac
License: Freeware | Size: 51.2 KB | Download (40): JDSA Download |
SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies This tool aims to identifying structural variations with both clustering and...
Platforms: *nix
License: Freeware | Size: 593.92 KB | Download (36): SVDetect Download |
GWCNV is a genome-wide algorithm for detecting CNV associations with diseases. It works directly on a transformation of intensity data. It is powerful and sensitive in detecting small CNV associations, and retains high power for large CNVs.
Platforms: *nix
License: Freeware | Size: 266.24 KB | Download (33): GWCNV Download |
Lucy is a program for DNA sequence quality trimming and vector removal. Its purpose is to process DNA sequence data acquired from DNA sequencers to prepare the data for downstream processing applications such as genome assembly.
Platforms: *nix
License: Freeware | Size: 1.38 MB | Download (33): Lucy For Linux Download |
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human...
Platforms: *nix
License: Freeware | Size: 7.34 MB | Download (35): Bowtie for Linux Download |
Bio::Tools::Run::PiseApplication::consensus is a Perl module. Bioperl class for: CONSENSUS Identification of consensus patterns in unaligned DNA and protein sequences (Hertz, Stormo) References: G.Z. Hertz and G.D. Stormo. Identification of consensus patterns in unaligned DNA and protein...
Platforms: *nix
License: Freeware | Size: 829.44 KB | Download (94): Bio::Tools::Run::PiseApplication::consensus Download |
GO::TermFinder is a Perl module that can identify GO nodes that annotate a group of genes with a significant p-value. This package is intended to provide a method whereby the P-values of a set of GO annotations can be determined for a set of genes, based on the number of genes that exist in the...
Platforms: *nix
License: Freeware | Size: 860.16 KB | Download (95): GO::TermFinder Download |
EnsEMBL::Web::Record is a family of modules used for managing a users persistant data in a database. SYNOPSIS Many web sites now encourage users to register and login to access more advanced features, and to customise a site to their needs. The EnsEMBL::Web::Record group of Perl modules is...
Platforms: *nix
License: Freeware | Size: 6.14 KB | Download (92): EnsEMBL::Web::Record Download |
Nowadays, the use of so-called RNA interference is a common technique applied by molecular biologists to determine the function of the many genes in our genome.Unfortunately, the design of oligonucleotides, the building blocks for this technique, is a time-consuming and error-prone task. iRNAi...
Platforms: Mac
License: Freeware | Download (94): iRNAi Download |
PGDSpider was built using the Java programming language as a conversion app for population genetics and genomics programs.
The software facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic...
Platforms: Windows
License: Freeware | Download (449): PGDSpider Download |
Gitools, is a framework for analysis and visualization of genomic data. Data and results are represented as browsable heatmaps. Gitools allows to import data directly from IntOGen and Biomart.
Platforms: Windows
License: Freeware | Size: 26.2 MB | Download (440): GiTools Download |
GNomEx is Genomic LIMS and Analysis Project Center designed by the Huntsman Cancer Institute for use by microarray and next generation sequencing core facilities and large research laboratories. KWs: Illumina, Affymetrix, Agilent, MAGE, MySQL/Flex...
Platforms: Windows
License: Freeware | Size: 26.8 MB | Download (445): GNomEx Download |