Bioinformatics tools

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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 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. more stack exchange communities plot - R: multiple x axis with annotations
plot - Control the size of points in an R scatterplot 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 Stack Exchange
Fitting polynomial model to data in R current community your communities Sign up or log in to customize your list. more stack exchange communities Stack Exchange Fitting polynomial model to data in 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 Trellis Graphs
g:Profiler - functional profiling of gene lists from large-scale experiments Welcome to g:GOSt! 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. g:Profiler - functional profiling of gene lists from large-scale experiments
Plus: a resource for protein phosphorylation and other post-translational modifications 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. 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 Bowtie: Tutorial Download and extract the appropriate Bowtie binary release into a fresh directory. Change to that directory. Performing alignments
SciRoKo Downloads SciRoKo Downloads SciRoKo is platform independent and runs in Windows, Linux and Mac OsX. 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 Systems Browser Search (use * as a wildcard) Query the database by first selecting a species (Mus musculus) and then entering a gene symbol (Spo11), a database identification number (MGI:1349669) or the Ensembl (ENSMUSG00000005883) identifier into the search field. If you use GermOnline for your research, please quote Lardenois and Gattiker et al. Database 2010.
GeneFisher2 Submission page
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
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
The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online. For easy access to commonly used genomes, drag from the bottom list to the top one · Save Favourites Human (Homo sapiens)Mouse (Mus musculus)Zebrafish (Danio rerio) Other available species Genome Browser
The EMBL Nucleotide Sequence Database
European Bioinformatics Institute | Homepage Whole-genome dataset for bread wheat now available in Ensembl Plants An improved genome sequence for bread wheat including more than 100,000 genes has been released in Ensembl Plants. Generated under the auspices of the International Wheat Genome Sequencing Consortium (IWGSC), the Chromosome Survey Sequence represents the most complete version of the wheat genome to date. ELIXIR launches as legal entity
BioMart
RCSB Protein Data Bank
SNP structure,function,disease:
genome browsers

DBGET
linux

The Gene Ontology
GeneCards V3 - Human Genes | Gene Database | Gene Search
ExPASy Proteomics Server
fastPHASE - Assets - Express Licenses - UW Center for Commercial
Haploview
PLINK: Whole genome data analysis toolset
BEAGLE genetic association analysis software
UNPHASED
Pfam: Search Pfam
Artemis: DNA Sequence Viewer and Annotation Tool - Wellcome Trus