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 search; [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:

 GRAIL-1.3 - exon prediction from genomic sequence (ORNL) [H] [P] [E] FGENEH - gene model construction from human genomic sequence (BCM Gene Finder) [H] [O] [P] [E] 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] [O] [P] [E] HEXON - search for human potential internal exons (BCM Gene Finder) [H] [O] [P] [E] MZEF - Predict human + strand internal coding exons (CSHL) [H] [O] [P] [E] HSPL - search for potential human splice sites (BCM Gene Finder) [H] [O] [P] [E] 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] [E] POLYAH - recognition of 3'-end cleavage and polyadenilation regions (BCM Gene Finder) [H] [E]
       


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] [E] TSSW - human PolII recognition using the TRANSFAC database (BCM Gene Finder) [H] [E] 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]
       


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]

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Page Curator: Kim C. Worley, Human Genome Center, Baylor College of Medicine (sl-help@dot.bcm.tmc.edu).
Last modified: Thu Oct 29 14:00:08 CST 1998
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