Resources

 

BioDeCypher Server



BioDeCypher ServerA local deployment of TimeLogic DeCypher Server, namely BioDecypher, is available to All Noble Foundation researchers. BioDeCypher server supports batch blast, Smith-Waterman, HMM and other model-based search algorithms. Featured modules on BioDecypher include:

DeCypherBLAST - for exhaustive genomic and protein sequence comparisons.

DeCypherHMM
- Hidden Markov Model analysis system for rapid protein classification using PFAM and other profile databases.

DeCypherSW
- rigorous Smith-Waterman methods find optimal local alignments across frameshifts and introns for homology modeling, microarray setup and siRNA studies.

GeneDetective
- aligns cDNA or amino acids to genomic DNA for accurate identification of gene models and splice variants.

Please note that the website interface has a limit on the number of sequences for each job submission. For example, one batch of blast job supports up to 2000 sequences. However, user can submit many jobs and wait for the results. Thus, virtually, there is no limit on the number of sequences that you can analyze using DeCypherBLAST on BioDeCypher server. Please email us if you would like to build custom blastable databases. We require you provide your sequences in fasta format or other standard formats. If you have any problem, please do not hesitate to send us messages.

[ Launch BioDecypher Server ]

 

NBCSC Web Services


PLAN (Personal bLAst Navigator) is a comprehensive web application for organizing, managing and mining sequence alignment results based on BLAST search.

[ Launch PLAN Server ]

 

NEST-PIPE (Noble EST-Pipeline) is an automated pipeline for the analysis of EST sequences. Features of NEST-PIPE include sequencing error detection, sequence cleaning, vector removal, sequence assembling, and functional annotation.

[ Launch NEST-PIPE ]

 

phpSSRMiner (Simple Sequence Repeat Marker Miner) effectively streamlines the process of SSR (Simple Sequence Repeat) identification, primer design, and in-silicon primer verification in a single web interface.

[ Launch phpSSRMiner ]

 

Other dedicated Servers: Please visit the Zhao bioinformatics gateway for more information.

[ Visit the Zhao Bioinformatics Lab ]