dcode.org

multitf.dcode.org

multiTF :: Identification of Transcription Factor Binding Sites Conserved in Multiple Species

Http:/ multitf . dcode . org. Identifies transcription factor binding sites conserved across multiple species. There are 3 diffrent ways to initiate a multiTF search:. Multiple sequence alignments of FINISHED sequences can be automatically submitted to multiTF from the results web page. Genome Alignment and Annotation Database; http:/ gala.cse.psu.edu/. Automatically forwards genome alignment data to Mulan for the subsequent multiTF post-processing. Return to previously submitted request. ID:.

mulan.dcode.org

Mulan :: MUltple sequence Local AligNment and visualization tool

Performs local multiple DNA sequence alignments of finished and draft-quality sequences. It identifies transcription factor binding sites evolutionarily conserved across multiple species. Including the reference sequence). ALL FINISHED SEQUENCES : TBA. DRAFT SECONDARY SEQUENCES : refine. Multiple contigs per sequence) DNA sequences with a finished reference. To increase alignments sensitivity. Useful for diverged sequences). Return to previously submitted request.

eshadow.dcode.org

eShadow :: phylogenetic shadowing

Ing of closely related species. I Ovcharenko, D. Boffelli, and G. Loots, eShadow: A Tool for Comparing Closely Related Sequences, Genome Research. 14(6), 1191-1198 (2004). 2 exons of LXRalpha: trimmed sequences. Return to previously processed request.

dire.dcode.org

DiRE :: identification of DIstant Regulatory Elements of co-regulated genes

Return to submitted job. Copy and paste gene names. Or accession numbers) ( example. Gene symbols (GATA2, PAX6, etc). GenBank mRNA (AK, NM , BC, X, etc). Nucleotide RefSeq (NM ). Protein RefSeq (NP ). UCSC Known Genes (uc000aaa.1). Select the source of background genes:. Copy and paste background genes. Top 3 ECRs promoter ECRs [default]. UTR ECRs promoter ECRs. NCBI DCODE.org Comparative Genomics Developments ( www.dcode.org.

creme.dcode.org

CREME 2.0 :: Cis-REgulatory Module Explorer

CREME has been retired and was replaced by DiRE. First, thank you all Creme users! Your interest in Creme has kept this service alive for over 4 years. Unfortunately, Creme has become outdated. It was operating on a very old version of the human genome. It was using outdated version of the TRANSFAC database. It was limited to the promoter regions of RefSeq genes only. Finally, we decided to retire the service. So bye-bye, Creme. Identifies proximal and Di. Based on the Enhancer Identification (EI) method.

ecrbrowser.dcode.org

ECR Browser :: Evolutionary Conservation of Genomes

Feature or position (chrN:from-to). In ECR Browser : Align your sequence. Zoom out 3x, i. Zoom in 3x,. Shift to the right,. Shift to the left, l. Flip the plot, g. Genome selection window, p. Parameters window, c. Highlight coreECRs, r. Reset parameters to defaults, f. Refresh the page, a. Additional alignments, m. Main gene annotation, z. I Ovcharenko, M.A. Nobrega, G.G. Loots, and L. Stubbs, Nucleic Acids Research, 32, W280-W286 (2004) [ PDF.

ecrbase.dcode.org

ECRbase :: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

We have recently modified ECR Browser alignments by including repetitive elements. All ECRbase ECRs correspond to new ECR Browser alignments now. Additionally, individual ECRs have been annotated according to their relationship to RefSeq genes and repetitive elements. Is the Database of Evolutionary Conserved Regions (ECRs), Promoters,. And Transcription Factor Binding Sites in Vertebrate Genomes. Created using ECR Browser. Of RefSeq and UCSC known genes. Transcription Factor Binding Sites.

zpicture.dcode.org

zPicture :: dynamic blastz alignment visualization

Is a dynamic alignment and visualization tool that is based on blastz. Alignment program utilized by PipMaker. ZPicture alignments can be automatically submitted to rVista 2.0. To identify conserved transcription factor binding sites. Genome Research, 14(3), 472-477, (2004). Multiple sequence alignment tool. Sequence and gene annotation from. FASTA file (.fa). Sequence and gene annotation from. FASTA file (.fa). OPTIONAL : ANNOTATION 1. Repeats are identified by lower-case letters. OPTIONAL : ANNOTATION 2.

synor.dcode.org

SynoR :: Genome Miner for Synonymous Regulation

Bps, but not more than. Note: The minimal distance is 3 bps, the maximal is 1000 bps.). Format: name count strand ). Fix the order of TFBS. List of available TFBS. Return to previously submitted request. NCBI DCODE.org Comparative Genomics Developments.

rvista.dcode.org

rVista 2.0 :: Identification of Evolutionary Conserved Transcription Factor Binding Sites

Http:/ rvista . dcode . org. Finding potential regulatory elements in noncoding regions of the human genome is a challenging problem. Analyzing novel sequences for the presence of known transcription factor binding sites or their weight matrices produces a huge number of false positive predictions that are randomly and uniformily distributed. rVista. Combines database searches with comparative sequence analysis, reducing the number of false positive predictions by 95%. If you have two sequence files.