Available Modules
Basic Information
  • DNA Coordinates: Use a GENE Page to enter coordinates
  • Nucleotide Sequence / Length: Use a GENE Page to find the Nucleotide Sequence and Length
  • Protein Sequence / Length: Use a GENE Page to find the Protein Sequence and Length
Sequence-based Similarity Data
  • BLAST: Find the top hits in BLAST using NCBI BLAST
  • CCD: Find COG Results from NCBI BLAST
  • T-Coffee: Run a multiple sequence alignment using T-Coffee
  • WebLogo: Find the sequence logo and analyze it
Cellular Localization Data
  • Gram Stain: Research Pubmed to find the gram stain of the organism
  • TMHMM: Plot the transmembrane topology
  • SignalP: Plot the signal peptide graph
  • LipoP: Predict lipoproteins and signal peptides
  • PSORT-B: Predict protien localization
  • Phobius: Plot the phobius posterior probabilities
Alternative Open Reading Frame
  • DNA Coordiantes: Change the DNA Coordinates if the ORF has been incorrectly determined
Structure-based Evidence
  • TIGRFAM: Search TIGRFAM Hidden Markov Model database for hits
  • Pfam: Find Pfam families within a sequence
  • PDB: Align sequences using Protein Data Bank
Enzymatic Function
  • KEGG: Find the KEGG Pathway and analyze the pathway map
  • MetaCyc: Find the Metabolic Pathway and analyze
  • EC Number: Use ExPASy ENZYME to locate the EC number and name
Duplication and Degradation
  • Paralogs: Use NCBI BLAST to find paralogs
  • Pseudogene: Research to find if the gene is a pseudogene
Horizontal Gene Transfer
  • Phylogenetic Tree: Use Phylogeny.fr to plot the phylogenetic tree from sequences
  • Gene Context: Find the Ortholog Neighborhood Region using IMG
  • Chromosome Viewer GC Heat Map: Analyze the GC heat map to find the characteristic and average GC%
RNA
  • Rfam: Find the Rfam number, score and pairwise alignment
Proposed Annotation
  • Note: Propose a new annotation to be placed in the note section of GENI-ACT and Genbank GBK