Bioinformatics tools
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. The first one is easy, use an apply function .
pairwise sequence alignment with R
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. 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
Trellis Graphs
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.
Bowtie: Tutorial
Download and extract the appropriate Bowtie binary release into a fresh directory. Change to that directory. Performing alignments
perl
Block Maker at the Fred Hutchinson Cancer Research Center BlockS WWW server. WARNING: This page is no longer supported, use at your risk.
Block Maker
genome browsers
linux
fastPHASE - Assets - Express Licenses - UW Center for Commercial
The program fastPHASE implements methods for estimating haplotypes and missing genotypes from population SNP genotype data. For more information: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
New to Artemis? Example of an Artemis screenshot.