Xanthomonas fuscans subsp. fuscans
FrameD


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.

Extra help and download information is available here.

Sequence
Choose the matrix:
Choose the replicon:
Enter the boundaries: begin: end: context (+/- nt):

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:
or
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: