BCM Search Launcher: Gene Feature Searches

BCM Search Launcher: Gene Feature Searches

Cut and paste nucleic acid sequence here (sequence only):

Sequence name/identifier (optional):

Choose search method:
[H] [O] [P] [E] = [H]:Help/description; [O]:full Options form; [P]:search Parameters; [E]:Example search
See Also: Species-Specific gene finding in [Drosophila, Nematode, Yeast, E. coli and Plants] or [Mouse, Fission Yeast and Arabadopsis].

Exon, Intron, and Gene Model Prediction:
GRAILEXP - Grail experimental gene discovery suite (ORNL) [H] [O]
GRAIL-1.3 - exon prediction from genomic sequence with RepeatMasker filtering (ORNL/UW) [H] [P] [E]
FGENES - Pattern based Human Gene structure prediction (multiple genes,: both chains) (BCM Gene Finder) [H]
FGENESH - HMM based Human Gene structure prediction (multiple genes,: both chains) (BCM Gene Finder) [H]
FGENES-M - Pattern based Human Multiple variants of Gene structure prediction) (BCM Gene Finder) [H]
Genie - gene finding based on Hidden Markov Models (LBNL/UCSC) [H] [O] [P] [E]
FEXH - human 5', internal, and 3' exon prediction (BCM Gene Finder) [H]
HEXON - search for human potential internal exons (BCM Gene Finder) [H]

MZEF - Predict human + strand internal coding exons (CSHL) [H] [O] [P] [E]
HSPL - search for potential human splice sites (BCM Gene Finder) [H]
NNSSP - human splice site prediction by neural network (LBNL) [H] [O] [P] [E]
RNASPL - search for exon-exon junction positions in human cDNA (BCM Gene Finder) [H]
POLYAH - recognition of 3'-end cleavage and polyadenilation regions (BCM Gene Finder) [H]
CDSB - search for E.coli protein coding genes (BCM Gene Finder) [H]
Promoter and Transcription Factor Binding Site Prediction:
TESS - search for transcription factor binding sites (U. Penn) [H] [O] [P] [E]
TSSG - human PolII recognition using the promotor.dat database (BCM Gene Finder) [H]
TSSW - human PolII recognition using the TRANSFAC database (BCM Gene Finder) [H]
Core-Promoter - TSS Human Core-Promoter Finder (CSHL) [H] [O] [P] [E]
NNPP / Eukaryotic - eukaryotic promoter prediction by neural network (LBNL) [H] [O] [P] [E]
NNPP / Prokaryotic - prokaryotic promoter prediction by neural network (LBNL) [H] [O] [P] [E]
MatInspector/TRANSFAC - transcription factor binding sites (AG BIODV) [H] [O] [P] [E]
POL3SCAN - eukaryotic PolIII recognition for tRNAs (U. Parma) [H] [E]
NSITE - Recognition of Regulatory motifs with statistics (BCM Gene Finder) [H]
Open Reading Frame Identification:
ORF ID / Eukaryotic - any start codon and minimum 25aa (U. Minn.) [H] [O] [P] [E]
ORF ID / Prokaryotic - Met start codon and minimum 100aa (U. Minn.) [H] [O] [P] [E]