A noise-resistant gene finder for prokaryotic and matured eukaryotic sequences

locates genes and frameshifts in procaryotic sequences and matured eukaryotic sequences (to predict and correct frameshifts in EST, EST clusters and cDNAs). Published research using this software should cite the following paper:

FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences
Thomas Schiex, Jérôme Gouzy, Annick Moisan, and Yannick de Oliveira
Nucl. Acids. Res. 2003 31: 3738-3741.

You can either select the Browse... button to choose a FASTA/raw DNA file or paste your sequence in the text area below. Sequences are limited to 500 kb.

Extra help and download information is available here.

Select one FASTA file:
Paste your
sequence in FASTA format:

Choose the probabilistic model

click here to learn a new one and add it to the system


FrameD behavior control more info
Compute mean expected prediction        Increased Sensitivity        Frameshit penalty Stop penalty    
Generate corrected sequence        Generate translated sequence         GC content
Matured eukaryotic sequences analysis (ATG start only)        TGA is not a stop codon    Default RBS pattern (16S side)    

Add (optional) protein similarities computed with NCBI-BLASTX (set alignment view option -m to 'tabular')
BLASTX tabulated output file:
Paste your
tabulated BLASTX output:
Confidence on BLASTX hit(s)

Output parameters (layout control)
Verbose                 Length per image (bp)        Overlap between succ. images (bp)  Offset 
First  nucleotide           Last nucleotide         X-resolution (pixels)        Y-resolution (pixels)
Score smoothing window             Score normalisation:
Select graphical elements:

Thomas Schiex
Last modified Apr 2, 2003