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.
To use GenSAS v2.0:
|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|
|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|
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.