GeneMark  
  A family of gene prediction programs developed at Georgia Institute of Technology , Atlanta, Georgia, USA.
What's New:
Pre-print
GeneMark-ETP
Supported by NIH
NIH

European Emergency Situation - applications for PhD in Bioinformatics

Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes
circular genome Novel prokaryotic genomic sequences can be analyzed by the self-training software tool GeneMarkS-2 (sequences longer than 50 Kb). For some species pre-trained model parameters are ready and available through the GeneMark.hmm. Metagenomic sequences and individual short sequences (sequences < 50 kb) can be analyzed by MetaGeneMark.
Gene Prediction in Eukaryotes
mouse Novel eukaryotic genomes can be analyzed by the self-training GeneMark-ES. The fungal mode of GeneMark-ES accounts for fungal-specific intron organization. GeneMark-ET integrates into GeneMark-ES information on mapped RNA-Seq reads. GeneMark-EP+ integrates into GeneMark-ES information on cross-species protein sequences. GeneMark-ETP integrates into GeneMark-ES both types of external information, RNA reads and cross-species proteins.
Gene Prediction in Transcripts
gel Sets of eukaryotic transcripts can be analyzed by GeneMarkS-T.
Gene Prediction in Viruses, Phages and Plasmids
virus Sequences of viruses, phages or plasmids can be analyzed either by GeneMarkS (sequences > 50 Kb) or MetaGeneMark (sequences < 50 kb)

All the software tools mentioned here are available for download.

The GeneMark software is a part of genome annotation pipelines at NIH NCBI (for prokaryotes) and DOE JGI (for eukaryotes) as well as others:
  • QUAST: assessment of genome assembly quality
    - uses GeneMarkS
  • MetAMOS: a tool for metagenome assembly and analysis
    - uses MetaGeneMark
Eukaryotic genome annotation pipelines:
  • MAKER2: uses GeneMark-ES along with SNAP and AUGUSTUS.
  • BRAKER1: integrates RNA-Seq reads
    -- uses GeneMark-ET and AUGUSTUS
  • BRAKER2: integrates known proteins
    -- uses GeneMark-EP+ and AUGUSTUS
  • BRAKER3: integrates RNA-seq reads and known proteins
    -- uses GeneMark-EP+ and AUGUSTUS

For more information see Background and Publications.

Borodovsky Group
Group news

Gene Prediction
Programs
Information Download Other Programs In silico Biology
International
Conferences
Bioinformatics
Studies at
Georgia Tech

Contact Us   |   Home