The Genome Sequence Annotation Server (GenSAS) is an online annotation tool that provides a customizable automated pipeline for whole genome structural annotation. Users can upload genomic sequence and select from a variety of tools for prediction of gene models and other structural features.
We are currently not providing new user accounts for this version of GenSAS.
We are almost done upgrading the user interface for GenSAS v3.0 and will grant new user accounts when the beta testing is complete in November. We thank you for your patience.
To use GenSAS v2.1:
|Tool Type||Tool Name||Description|
|Intrinsic Gene Prediction||Genscan||Predicts the exon-intron locations within genes|
|FGENESH||HMM-based gene structure prediction for eukaryotes (Cannot run analysis, but will accept upload of FGENESH output files)|
|Augustus||Predicts eukaryotic genes including 5’ and 3’ UTR sequences and alternative genes|
|Glimmer||Predicts coding regions for prokaryotes and viruses|
|GlimmerM||Based on Glimmer, GlimmerM is specific for eukaryotes and the exons in those genomes|
|SNAP||Gene finder for prokaryotes and eukaryotes|
|Extrinsic Gene Prediction||Transcript BLAST||
BLAST against transcript databases from NCBI. The following databases are available:
BLAT uses an index derived from assemblies of entire genomes to predict genes. The following databases are available:
BLAST against protein databases from NCBI. The following databases are available:
|Other Genetic Features||getorf||Finds ORFs based on start and stop codons|
|SSR Server||Finds simple sequence repeat sequences|
|tRNAscan||Identifies tRNA sequences|
|Misc. Tools||RepeatMasker||Masks interspersed repeats and low complexity DNA sequences|
|RepeatModeler||De novo repeat identification and modeling tool|
|GFF3 Importer||Allows for addition of previously run data to be viewed as Track in graphical results interface|
In the future, GenSAS will migrate approved gene models to a Chado database which can then be visualzed with other GMOD tools including GBrowse and Tripal. GenSAS will also encapsulate more complex workflows such as pre-processing of a training set for some gene prediction tools as well as a consensus program to combine and prioritize gene models from various tools.