NOVELTIES
ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others).ANNOVAR is written in Perl and can be run as a standalone application on diverse hardware systems where standard Perl modules are installed. Registration not required.
Click here for more informationsPublished on 2012-02-12 11:46:27
VAAST (the Variant Annotation, Analysis and Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. Registration required.
Click here for more informationsPublished on 2012-02-12 11:39:11
PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important. The performance of PROVEAN is comparable to popular tools such as SIFT or PolyPhen-2. Registration not required.
Click here for more informationsPublished on 2012-02-12 11:36:27
PHAST is a freely available software package (Cornell University) for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel).Like algorithms that assess protein-coding genes, they evaluate variants on the basis of how often the sequence changes between species
Click here for more informationsPublished on 2012-02-12 11:36:03
Genomic Evolutionary Rate Profiling (GERP) identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as "Rejected Substitutions". Registration not required.
Click here for more informationsPublished on 2012-02-12 11:35:31
SIFT (Sorting Intolerant From Tolerant) predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. Registration not required.
Click here for more informationsPublished on 2012-02-12 11:34:14
Report on Carcinogens, U.S. Department of Health and Human Services, Public Health Service, National Toxicology Program . Registration not required.
Click here for more informationsPublished on 2012-02-02 04:52:32
Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. Although originally designed for visualizing genomic data, it can create figures from data in any field. It requires PERL software language. Registration not required.
Click here for more informationsPublished on 2012-01-20 10:25:05
Here you can view the current vacancies and find all of the information you need about working for the University of Cambridge, UK Registration not required.
Click here for more informationsPublished on 2012-01-20 04:10:11
The GSEA algorithm implemented in MeV is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA software uses the Molecular Signatures Database (MSigDB), a collection of annotated gene sets. Registration required.
Click here for more informationsPublished on 2012-01-18 08:55:04
Galaxy is an open, web-based platform for data intensive biomedical research, now available as a "cloud computing" resource Whether on this free public server or your own instance, you can perform, reproduce, and share complete analyses. Registration required.
Click here for more informationsPublished on 2012-01-18 06:35:45
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
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