Given Affymetrix CEL files, AffyDEGfinder finds differentially expressed genes and runs clustering, annotation, and GO and KEGG enrichment analysis for them using R/Bioconductor through Chipster. This workflow consists of the following steps:

• Normalize the data using rma (normalized.tsv)
• Run a statistical test on the normalized data using empirical bayes (two-sample.tsv)
• Perform hierarchical clustering (hc-genes.txt, hc-chips.txt)
• Write out a heatmap image (heatmap.png)
• Annotate results (annotations.tsv)

This service extracts documents from indexed document corpora (e.g. MedLine). It is part of the AIDA (Adaptive Information Disclosure Application) toolbox for knowledge extraction and knowledge management that is being developed for the Dutch e-science and bioinformatics projects VL-e and BioRange.

The service is based on the Lucene libary. It was created by Edgar Meij.

BioMart web service provides unified access to several databases housed at EBI/Sanger such as Ensembl Vertebrates, Ensembl Bacteria, Ensembl Protists, Ensembl Metazoa, Ensembl Variation, Ensembl Vega, Uniprot, PRIDE, HGNC & EU Rat Mart. The service also provides federated access to number of databases outside EBI including Reactome Pathways, PepSeeker, Gramene and Wormbase. For an up-to-date list of datasets, please visit, http://www.biomart.org

Uses the DDBJ's UniProt BLAST service that forms part of its Web API for Bioinformatics pages.

Description

Find local similarity with the BLAST algorithm between a query sequence of protein and a reference database of proteins.

Usage

You need to provide the following input arguments to the service:

This BLASTatlas service creates maps of genome homology of a list of sequences against a reference
genome using either blastp, blastn, tblastn, or blastx.

The resolution is per-residue or per nucleotide depending on the regime of the blast
search: For each annotation in the reference genome, the best hit in the database
genome is found using one of the above algorithms. Each matching or mismatching
residue/nucleotide of the best hit (based on BLAST score) is then mapped back to the
genome sequence, using the coordinates provided in the annotations.

BLASTn finds regions of similarity between a nucleotide query sequence and a nucleotide sequence database.
Computations are done on the Vital-IT cluster (SIB).
Most NCBI BLAST (2.2.17) options are available.
Most SIB databases are available: STS, EST, HTG, refseq, repbase, ...

INPUT: nucleotide sequence(s) + choose a database
OUTPUT: BLAST output

BLASTp finds regions of similarity between an amino acid query sequence and a protein sequence database.
Computations are done on the Vital-IT cluster (SIB).
Most NCBI BLAST (2.2.17) options are available.
Most SIB databases are available: Uniprot, UniRef, organism proteomes, refseq protein, nrl3D, ...

INPUT: protein sequence(s) + choose a database
OUTPUT: BLAST output

blastProDom performs a blast (blastx or blastp) on the protein domain family database ProDom : enter a sequence (nucleotides or proteins, raw or fasta format) and it returns a blast output with the name of the families corresponding to the hits found, and a URL to get the image visualizing the blasted domains on the protein.

A perl script is available to run this webservice from your computer. Please install SOAP Lite before.

BLASTx finds regions of similarity between a nucleotide query sequence translated in all reading frames and a protein sequence database.
Computations are done on the Vital-IT cluster (SIB).
Most NCBI BLAST (2.2.17) options are available.
Most SIB databases are available: Uniprot, UniRef, organism proteomes, refseq protein, nrl3D, ...

INPUT: nucleotide sequence(s) + choose a database
OUTPUT: BLAST output