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Pairwise sequence alignment with R. 2.3 years ago by New Zealand Hi Laksmi,

pairwise sequence alignment with R

Plot - R: multiple x axis with annotations. Current community your communities Sign up or log in to customize your list.

plot - R: multiple x axis with annotations

Plot - Control the size of points in an R scatterplot. Current community your communities Sign up or log in to customize your list. more stack exchange communities.

plot - Control the size of points in an R scatterplot

Fitting polynomial model to data in R. Current community your communities Sign up or log in to customize your list. more stack exchange communities.

Fitting polynomial model to data in R

Trellis Graphs. The lattice package, written by Deepayan Sarkar, attempts to improve on base R graphics by providing better defaults and the ability to easily display multivariate relationships.

Trellis Graphs

In particular, the package supports the creation of trellis graphs - graphs that display a variable or the relationship between variables, conditioned on one or more other variables. The typical format is graph_type(formula, data=) where graph_type is selected from the listed below. formula specifies the variable(s) to display and any conditioning variables . G:Profiler - functional profiling of gene lists from large-scale experiments. Welcome to g:GOSt!

g:Profiler - functional profiling of gene lists from large-scale experiments

First time? See our welcome note. g:GOSt performs functional profiling of gene lists using various kinds of biological evidence. The tool performs statistical enrichment analysis to find over-representation of information like Gene Ontology terms, biological pathways, regulatory DNA elements, human disease gene annotations, and protein-protein interaction networks. Its output is a tabular graphic where genes are shown in columns, functions in rows, and coloured table cells show functional associations.

Examples. Plus: a resource for protein phosphorylation and other post-translational modifications. Protein, Sequence, or Reference Search: Protein Searches retrieve lists of proteins and their modification types based on protein name or ID, protein type, domain, cellular component, and MW range.

Plus: a resource for protein phosphorylation and other post-translational modifications

Sequence searches retrieve lists of proteins and sequences containing specified sequences, degenerate motifs, and domains. Worm Interactome Version 8. Bowtie: Tutorial. Download and extract the appropriate Bowtie binary release into a fresh directory.

Bowtie: Tutorial

Change to that directory. SciRoKo Downloads. SciRoKo is platform independent and runs in Windows, Linux and Mac OsX.

SciRoKo Downloads

It has, however, primarily been developed for Windows, if you encounter any problems in Linux or Mac OsX please try the Windows version. If you have any problems with the Windows version, please contact me at the eMail address below. Download SciRoKoCo The command line version of the SciRoKo SSR-search module! Download Design Primer The perl script DesignPrimer can be used to automatically design PCR primer pairs for the SciRoKo output. Run SciRoKo in Windows: 1.) 2.) Protein, Sequence, or Reference Search. Systems Browser. GeneFisher2 Submission page. Perl. Block Maker. Block Maker at the Fred Hutchinson Cancer Research Center BlockS WWW server.

Block Maker

WARNING: This page is no longer supported, use at your risk. Alternative multiple sequence alignment methods. CODEHOP. NOTICE: This version of CODEHOP is no longer maintained. The current version is iCODEHOP at U. Pittsburgh PCR primers designed from protein multiple sequence alignments Getting started Full Help file The CODEHOP algorithm The CODEHOP manuscript Genes identified using CODEHOP The input should be a set of local multiple alignments (blocks) of a group of related protein sequences. The alignments must be in Blocks Database format, such as in Block Maker output. Genetic code. National Center for Biotechnology Information.

Genome Browser. The EMBL Nucleotide Sequence Database. European Bioinformatics Institute. BioMart. RCSB Protein Data Bank. A Structural View of Biology This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data.

The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond. Use this website to access curated and integrated biological macromolecular information in the context of function, biological processes, evolution, pathways, and disease states.

Take an Interactive Tour of the PDB 3D Structure: Jmol The Jmol molecular viewer offers several options for display and analysis. SNP structure,function,disease: Genome browsers. DBGET. Linux. The Gene Ontology. GeneCards V3 - Human Genes. ExPASy Proteomics Server. FastPHASE - Assets - Express Licenses - UW Center for Commercial. The program fastPHASE implements methods for estimating haplotypes and missing genotypes from population SNP genotype data. Licensing Information fastPHASE is one of the many software programs and tools created at the University of Washington available through our Express Licensing Program.

These agreements have standard terms and conditions that allow for rapid licensing by companies, organizations, or individuals Academic License License. Haploview. Overview Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently supports the following functionalities: LD & haplotype block analysis haplotype population frequency estimation single SNP and haplotype association tests permutation testing for association significance implementation of Paul de Bakker's Tagger tag SNP selection algorithm.

Automatic download of phased genotype data from HapMap visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. The best way to become familiar with Haploview is to get the software and go through the tutorial. PLINK: Whole genome data analysis toolset. BEAGLE genetic association analysis software. Pfam: Search Pfam. Artemis: DNA Sequence Viewer and Annotation Tool - Wellcome Trus. New to Artemis? Example of an Artemis screenshot. zoom The Artemis manual explains how to install and run Artemis and what most parts of the program do. The FAQs may help if you are experiencing problems with Artemis.