OREGON STATE UNIVERSITY

CGRB Program Documentation and Man Pages

 

These links are provided to users of the CGRB at Oregon State University. Please do not share files or links provided on this page to groups outside the university without CGRB approval.

  • How to submit jobs to the infrastructure can be found in the file "cgrb_infrastructure.pdf"
  • CGRB File Upload and Download:
    • Please use the server "files.cgrb.oregonstate.edu" to transfer data. This machine is setup for fast transfers and this will ensure there is no congestion on the "shell" access machine. This machine is not for general web services. This machine is strictly for upload and download of files. Please limit the number of concurrent upload/downloads per users. Examples of how to upload and download data using files.cgrb.oregonstate.edu can found in the file "cgrb_files_access.pdf". Please do not upload any copyrite material.
  • Boxshade:  Multiple Sequence Alignment shading
  • CAP3: Generates contigs from overlapping DNA sequences
  • ClustalW:  Generates Multiple Sequence Alignments
  • ClustalX:  X-Windows version of ClustalW
  • Consed: tool for viewing, editing, and finishing sequence assemblies created with phrap
  • EMBOSS: Diverse suite of bioinformatics utilities
  • FASTA34: Bill Pearson FASTA package
  • Geneious Pro: GUI bioinformatics analysis
  • HMMER [PDF]: profile HMMs for protein sequence analysis
  • Illumina Manuals: Documentation for Illumina analysis pipeline software
  • InterPro: Integrated Resource Of Protein Domains And Functional Sites
  • Mason:  A high performance dynamic web site authoring system
  • MOSAIK: MOSAIK is a reference-guided assembler
  • MPI:  Parallel Message Passing Interface
  • Mummer:  Rapid alignment of very large DNA or protein sequences (UNIX program)
  • Muscle:  Multiple sequence comparison by log-expectation
  • NCBI Software: blastall, formatdb, etc.
  • PAUP
  • PCAP: Generates contigs for large-scale sequencing projects
  • Phrap: program for shotgun sequence assembly
  • Phred:  DNA base caller
  • Phylip:  PHYLogeny Inference Package
  • PROBCONS:  Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
  • RBS Finder:  Ribosome Binding Site Finder
  • Roche Manuals: Documentation for Roche 454 GS Junior sequencer
  • Sequin: NCBI sequence submission tool
  • tacg:  find patterns in DNA sequences (UNIX program)
  • T-Coffee: Multiple Sequence Alignment
  • TMHMM:  Identify membrane-spanning regions using Hidden-Markov Models
  • Vienna RNA Package:  RNA folding routines