GENIO/seq - A Non Redundant Eukaryotic Gene Database of
Annotated Sites and Sequences
Niels Mache, Paul Levi
Institute of Parallel and Distributed High-Performance Systems (IPVR)
Breitwiesenstr. 20-22, 70565 Stuttgart, Germany
e-mail: mache at struktur.de
Phone: +49 711 896656 0, Fax: +49 711 896656 10
Keywords: eukaryotic genes, DNA sequence database, GenBank, DNA analysis, gene finding.
GENIO/seq is a non redundant database of annotated and consistence checked genes. The database was compiled by screening GenBank release 102. It is organized into organism specific (Homo Sapiens, Primates, Plants, Maize) and single/multi-exon genes. All sequences meet the minimal criteria: first exon begins with ATG, last exon ends with stop codon and no other in-frame stop codons, splice sites match donor-acceptor GT-AG consensus. A collection of script programs are provided to collect specific DNA sequences from the database and convert it into FASTA sequence files. The following features and statistics are supported: Statistics of intron/exon distribution, codon usage, oligonucleotide frequencies and splice site odds ratio are provided with the database. GENIO contains 558 multi-exon Homo Sapiens genes (3680 exons, 14.0 Mbp) compiled from 495 GenBank entries. GENIO database and the supplied software will be available to the public in March 1998.
This work is part of the joint research project Computer aided automatic sequence analysis of the human genome, sponsored by the Federal Ministry of Education, Science, Research and Technology (BMBF), BMBF-Förderkennzeichen FKZ 01KW9631/6.
 
 

RECOMB-98 Poster:

RECOMB-98 poster (postscript file, zipped)
RECOMB-98 poster (GIF file small)
RECOMB-98 poster (GIF file large)
 

GENIO/seq software and sequence files:

scripts and programs
 
Due to disk space limitations only Homo Sapiens sequences are currently available


GENIO suite:

 
GENIO/seq  - A Non-Redundant Eukaryotic Gene Database of Annotated Sites and Sequences
GENIO/scan - EST/CDS Guided Identification of Genes in Human Genomic DNA
GENIO/lookup - masked (eukaryotic) EST search with BLAST
GENIO/cover  - GENIO/scan EST Coverage Analysis of Currently Known Eukaryotic Coding Sequences
GENIO/logo  - Nucleic and Amino Acid Sequence Logos
GENIO/splice - Splice Site and Exon Prediction in Human Genomic DNA
GENIO/frame - Frame Shift Analysis and Sequencing Error Detection
Important information: Due to security and privacy requirements your data sent as well as the data generated during GENIO request(s) will be erased automatically 15 minutes after your request. Please download your data files within 15 minutes.

Problems, suggestions, remarks?
Feel free to send an email to Niels Mache (mache at struktur.de)  (my home page is here)