Bioinformatics tools

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Pairwise sequence alignment with R. 2.3 years ago by New Zealand Hi Laksmi, It's not quite clear from your questoin, but do you want to do a pairwise alignment of each of your 90 sequences against a particular sequence (ie seq2[[1]] v seq1 then seq2[[2]] v seq1 in your example) or you want to do all the possible pairwsie comparisons between your 90 sequences.

pairwise sequence alignment with R

Plot - R: multiple x axis with annotations. Plot - Control the size of points in an R scatterplot. 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. 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. 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. Reference searches retrieve lists of literature references specified by authors, proteins, or PubMedIDs. Worm Interactome Version 8. Bowtie: Tutorial. Download and extract the appropriate Bowtie binary release into a fresh directory.

Bowtie: Tutorial

Change to that directory. Performing alignments. 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. 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. 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. 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.

RCSB Protein Data Bank

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. 3D Structure: Jmol. 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.

fastPHASE - Assets - Express Licenses - UW Center for Commercial

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

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. 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.