search for: uniprot

..."knows" of his whole document, but I seem not to be able to find a proper solution. So, my question is: How do I restrict a call of getNodeSet to just a XMLNode and not the whole document it was retrieved from? I use the XML and RCurl packages. The document I speak of is downloaded from uniprot.org, a protein knowledge server well known to biologists. The lamentably somewhat lengthy code follows: library(XML) library(RCurl) getEntries <- function( uniprot.xml, uniprot.error.msg.regex='^ERROR' ) { # Uniprot's dbfetch can be asked to return several entry tags in the same...

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow wit...

Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some

...face arules Mining Association Rules and Frequent Itemsets base The R Base Package Biobase Biobase: Base functions for Bioconductor biomaRt Interface to BioMart databases (e.g. Ensembl, Wormbase, Gramene and Uniprot) Biostrings String objects representing biological sequences, and matching algorithms boot Bootstrap R (S-Plus) Functions (Canty) Category Category Analysis CCl4 Carbon Tetrachloride (CCl4) treated hepatocytes...