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.

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zPicture :: dynamic blastz alignment visualization | zpicture.dcode.org Reviews

<META> DESCRIPTION

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.

<META> KEYWORDS

1 dcodeorg

2 ecr browser

3 ecrbase

4 mulan

5 zpicture

6 dire

7 synor

8 multitf

9 array2bio

10 eshadow

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dcodeorg,ecr browser,ecrbase,mulan,zpicture,dire,synor,multitf,array2bio,eshadow,instructions,example,human rat fugu,and human rat,alignment,multi zpicture,sequence 1,upload,ucsc genome browser,paste sequence,in fasta format,ncbi accession #,sequence 2

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zPicture :: dynamic blastz alignment visualization | zpicture.dcode.org Reviews

https://zpicture.dcode.org

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.

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zpicture.dcode.org

1

Description

http://zpicture.dcode.org/zpDescription.php

ZPicture: blastz-based alignment and visualization tool. ZPicture is a pairwise alignment and visualization tool that compares two sequences using the local alignment program BlastZ (Schwarz et al. 2003) and displays the gapless blocks of shared homology as unconnected dots (PIP) or smooth trace (VISTA) conservation plots. Unlike any other available alignment visualization tool, zPicture allows for customized real-time processing of alignment data. Also, zPicture allows easy extraction of ECR sequences a...

2

zPicture :: dynamic blastz alignment visualization

http://zpicture.dcode.org/multiz.php

Zpicture.dcode.org/multiz.php. Is a multi-sequence version of zPicture alignment and visualization tool. Please note that it is not possible to submit multi-zPicture alignments to rVista - use Mulan ( mulan.dcode.org. Pairwise sequence alignment tool. TOTAL NUMBER OF SEQUENCES. Including the reference sequence). Return to previously submitted request. Dcodeorg Comparativve Genomics Center.

3

zPicture :: dynamic blastz alignment visualization

http://zpicture.dcode.org/helpAnno.php

Annotation files include positional information for the nucleotide. Location of known coding exons (CDS), untranslated regions (UTR) or any. Other DNA features known for the input sequence contigs. zPicture. Reconstitutes gene annotation from each gene description provided. Gene. Description for an mRNA transcript starts with a header line and ends. With an emply line. First symbol in the header line (. Indicates the direction of the gene transcript relative to the input.

4

zPicture: Fetching UCSC sequences, repeats and genes annotation

http://zpicture.dcode.org/ucscFetch.php?seqInd=1&id=08150231048461&prog=zpicture

Select a species, genomic interval and genome assembly freeze from the UCSC Genome Browser. Link will open in a new window). Describe selected region using the form below. Known Genes From UCSC. Submit your request for verification. Please read zPicture instructions. Or us know ( dcode@ncbi.nlm.nih.gov. If you encounter troubles using this form.

5

zPicture instructions

http://zpicture.dcode.org/zpInstructions.html

How to use zPicture ( zpicture.dcode.org. Downloading Sequences from NCBI. Downloading Sequences and Gene Annotation from UCSC Genome Browser. Annotation of Repetitive Elements. Return to Previously Submitted Request. Obtaining sequences underlying ECRs. Identification of Evolutionary Conserved Binding Sites). Modifying Annotation and Sequence Titles). Identification of Evolutionary Conserved Regions (ECRs). Blastz and Textual Alignment Files. Access to the Input Sequences. There are two options for uplo...

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dire.dcode.org

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

http://dire.dcode.org/cite.php

Return to submitted job. If you find the results useful for your research, please cite DiRE as. Gotea, V. and I. Ovcharenko ( 2008. DiRE: identifying distant regulatory elements of co-expressed genes. Nucleic Acids Research. Doi:10.1093/nar/gkn300 [ Abstract. NCBI DCODE.org Comparative Genomics Developments ( www.dcode.org.

dire.dcode.org

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

http://dire.dcode.org/index.php?id=example

The requested ID is not valid. Please let us know ( dcode@ncbi.nlm.nih.gov.

dire.dcode.org

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

http://dire.dcode.org/return.php

Return to submitted job. Please enter a 16-digit request ID. To return to your previously submitted job:. NCBI DCODE.org Comparative Genomics Developments ( www.dcode.org.

dire.dcode.org

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

http://dire.dcode.org/details.php

Return to submitted job. Regulation of gene expression in eukaryotic genomes is established through a complex cooperative activity of proximal promoters and distant regulatory elements (REs) such as enhancers, repressors, and silencers. We developed a web server called DiRE. Lements, based on the Enhancer Identification (EI) method. Allows users to start their analysis with raw microarray expression data. Continue to: screen shots.

bitnos.com

Bitnos - Dna Alignment

http://www.bitnos.com/dna-alignment

Search nucleotide subjects using a nucleotide query. BLAST nucleotide (BLASTN) searches nucleotide subjects using a nucleotide query. Multiple Sequence Alignment is the arrangement of several protein or nucleic acid sequences with postulated gaps so that similar residues (in one-letter code) are juxtaposed. Sequencing and assembly software. Multiple sequence alignment with hierarchical clustering. Printouts from multiple-aligned protein or DNA sequences. PRALINE is a multiple sequence alignment program w...

bx.psu.edu

CCGB | projects

http://bx.psu.edu/projects

Tasmanian Tiger Sequencing Project. Tools for manipulating biological data, particularly multiple sequence alignments. These are web browser based software tools that CCGB members have developed or contributed to. UCSC Genome Browser Mirror. Local partial mirror of the UCSC Genome Browser. Visualization tools for bacterial genome alignments. Evolutionary test of predicted exons. Genome alignment and annotation database. Metaserver for integrative analysis of genomic data. 124; Privacy and Legal Statements.

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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.

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