NOVELTIES
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. It runs on Intel-based computers running Linux or Mac OS X and that have GCC 4.0 or greater installed. It requires SAMtools. Registration not required.
Click here for more informationsPublished on 2012-01-18 06:24:30
The RDXplorer (Read Depth eXplorer) is a computational tool based on LINUX/UNIX/MAC OS X for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. It requires SAMtools and Python programming language v 2.6 or further. Registration not required.
Click here for more informationsPublished on 2012-01-18 06:17:49
FusionSeq programs are written in C and constitute a tri-modular computational framework to detect fusion transcripts from paired-end RNA-sequencing. Registration not required.
Click here for more informationsPublished on 2012-01-18 06:08:51
TopHat is a Linux or OS X program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is designed to work with reads produced by the Illumina Genome Analyzer, although it was successful used with reads from other technologies. TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. It requires Bowtie, SAMtools an Python programming language v. 2.4 or higher in the computer path. Registration not required.
Click here for more informationsPublished on 2012-01-18 06:01:29
SAMtools provide various utilities for manipulating alignments in the Sequence Alignment/Map (SAM) format, including sorting, merging, indexing and generating alignments in a per-position format. Registration not required.
Click here for more informationsPublished on 2012-01-18 04:42:42
GATK (Broad Institute) is a structured programming framework designed to enable rapid development of efficient and robust analysis tools for next-generation DNA sequencers and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. The GATK s a Java-based tool intended for use on Linux (and other POSIX compatible) platforms. Registration not required.
Click here for more informationsPublished on 2012-01-18 04:28:12
BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads. Registration not required.
Click here for more informationsPublished on 2012-01-16 05:50:03
BLAST nucleotide (BLASTN) searches nucleotide subjects using a nucleotide query. Registration not required.
Click here for more informationsPublished on 2012-01-09 04:29:25
"How people in science see each other" is an absolutely brilliant and hilarious chart created by @biomatushiq about how people in science see each other. Registration not required.
Click here for more informationsPublished on 2011-11-25 01:32:40
The Mouse Genomes Project aims to use new sequencing technologies to sequence the genomes of 17 key mouse strains. We are releasing the raw sequence data, SNPs, short indels, structural variants and assemblies of each strain. Registration not required.
Click here for more informationsPublished on 2011-11-23 12:02:47
The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research. Its goal is the establishment of a Rat Genome Database, to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data. RGD was created to serve as a repository of rat genetic and genomic data, as well as mapping, strain, and physiological information. It also facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Registration not required.
Click here for more informationsPublished on 2011-11-23 12:01:08
Sage Bionetworks is an open-access online resource that helps researchers of all stripes access network biology. The Sage Bionetworks Commons will be used to integrate diverse molecular mega-datasets, to build predictive bionetworks and to offer advanced tools proven to provide unique new insights into human disease biology. Registration required.
Click here for more informationsPublished on 2011-10-19 10:57:43
The Gene Quantification page describes and summarises all technical aspects involved in quantitative gene expression analysis using real-time qPCR & qRT-PCR. Registration not required.
Click here for more informationsPublished on 2011-10-11 12:36:52
OligoAnalyzer is a web application from IDT that provides the opportunity to analyze hairpin and self-dimer of existing primers this site. Moreover this site allows you to BLAST the sequence against NCBI's database and measure the impact of incorporating 5'-modifications into the sequence. The oligos can then be ordered directly. Registration not required.
Click here for more informationsPublished on 2011-10-06 10:27:03
LALIGN/PLALIGN find internal duplications by calculating non-intersecting local alignments of protein or DNA sequences. LALIGN shows the alignments and similarity scores, while PLALIGN presents a "dot-plot" like graph. Registration not required.
Click here for more informationsPublished on 2011-10-06 10:09:52
AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation. Registration not required.
Click here for more informationsPublished on 2011-10-04 15:13:41
The purpose of the MAQC project is to provide quality control tools to the microarray community in order to avoid procedural failures and to develop guidelines for microarray data analysis by providing the public with large reference datasets along with readily accessible reference RNA samples. Registration not required.
Click here for more informationsPublished on 2011-10-04 14:51:22
PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. Registration not required.
Click here for more informationsPublished on 2011-10-04 14:30:41
An Online Catalog of Human Genes and Genetic Disorders. OMIM is supported by a grant from NHGRI. Registration not required.
Click here for more informationsPublished on 2011-09-30 11:19:23
We are not a software development lab, but we develop a lot of software tools to support our research and make it all available for anyone to use and repurpose. Registration not required.
Click here for more informationsPublished on 2011-09-19 17:31:51
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