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ARTADEdb

http://omicspace.riken.jp/ARTADE/

Description :
The tiling array is a powerful tool to discover the unknown transcripts that were essentially undetectable by construction of cDNA libraries or by strictly sequence-based gene predictions. Here we introduce a database named ARTADEdb containing transcriptional structures elucidated by our original statistical method ARTADE which estimates exon/intron structures of structurally unknown genes based on both tiling array data and genomic sequence data. By applying it to genome-wide tiling array data from four tissues in Arabidopsis, 14,782 transcriptional units (TUs) including 5,250 novel TUs found in the intergenic regions were registered in ARTADEdb. As 84.4% of the novel TUs were verified to be actually expressed by comparison with Arabidopsis UniGene clusters, the results are of benefit for researchers hunting for novel genes and their functions. The predicted genes were annotated with information on their expression values, significances of the expressions, nucleic- and amio-acid sequences, functionally known references, and were clustered as TUs based on their genomic positions. For the userís convenience, the gene records are related to available mutants, full-length cDNAs, literature-based related genes, and ontologies. In the database system, the genes can be searched by specifying keywords related to the above-mentioned annotations, filtered by expression cutoffs or other criteria, and the resulting list is ranked based on various parameters. The system also supplies a primer-designing function so that promising candidate genes are quickly verified experimentally. The database is integrated in our original data-retrieval framework named GPS: Genome?Phenome Superhighway, and is accessible at http://omicspace.riken.jp/ARTADE/.

trome, trEST and trGEN

ftp://ftp.isrec.isb-sib.ch/pub/databases/

Description :
Databases of predicted human protein sequences

EUGENE HOM

http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl

Description :
EUGENE HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.

IBM Bioinformatics and Pattern Discovery Group

http://cbcsrv.watson.ibm.com/Tspd.html

Description :
Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

TACT

http://www.jbirc.aist.go.jp/tact/

Description :
Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.

Taverna

http://taverna.sourceforge.net/

Description :
taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators.

TIGR Software Tools

http://www.tigr.org/software/

Description :
A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).

AGenDA

http://bibiserv.techfak.uni-bielefeld.de/agenda/

Description :
AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.

AMIGene

http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php

Description :
Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.

AUGUSTUS

http://augustus.gobics.de/submission

Description :
AUGUSTUS is a eukaryotic gene prediction tool for modeling intron length distribution, and searching for motifs and multiple splice variants. It is particularly effective with larger sequences. It can be run through a web interface, or downloaded and run locally.

BAGEL

http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php

Description :
BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.

BLAST

http://www.ncbi.nlm.nih.gov/BLAST/

Description :
Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

CPC

http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp

Description :
CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.

DGSF

http://sdmc.lit.org.sg/promoter/dragonGSF1_0/genestart.htm

Description :
Dragon Gene Start Finder (DGSF) predicts promoters and transcription start sites (TSS) within CpG islands for mammalian DNA sequences.

DNAtools

http://hydra.icgeb.trieste.it/~kristian/dna/

Description :
DNAtools include predicting DNA curvature; plotting physicochemical, statistical, or locally computed paramaters along DNA sequences; producing a 3-D model of a DNA sequence; searching an intron database.

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