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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

The first one is easy, use an apply function. I don't have bioconductor on this computer, so this isn't tested, but something like sapply( seq2, function(x) pairwiseAlignment(toupper(c2s(x)), seq1string)) ) It's probably more readible if you define a function first: 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 graph_type(formula, data=) where graph_type is selected from the listed below. formula specifies the variable(s) to display and any conditioning variables . For example ~x|A means display numeric variable x for each level of factor A. y~x | A*B means display the relationship between numeric variables y and x separately for every combination of factor A and B levels. G:Profiler - functional profiling of gene lists from large-scale experiments.

Plus: a resource for protein phosphorylation and other post-translational modifications. 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 The Bowtie source and binary packages come with a pre-built index of the E. coli genome, and a set of 1,000 35-bp reads simulated from that genome. To use Bowtie to align those reads, issue the following command. If you get an error message "command not found", try adding a ./ before the bowtie. bowtie e_coli reads/e_coli_1000.fq The first argument to bowtie is the basename of the index for the genome to be searched. Depending on your computer, the run might take a few seconds up to about a minute.

Next, issue this command: 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. Protein, Sequence, or Reference Search. Systems Browser. GeneFisher2 Submission page. Block Maker. CODEHOP. 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. 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. 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 An academic license is available to users at academic and nonprofit research institutions at no charge. Commercial License License Download the Express License (PDF file) by clicking on the button to the right, sign it, and return it to UW Center for Commercialization. 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. 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.