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NAR Web Server Issue 2003

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Found 114 links

Displaying 9 links

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TRACTSTool Content

http://bioportal.weizmann.ac.il/tracts/tracts.html [open in a new window]

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DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection

TRACTS calculates the frequencies, locations and lengths of all binary tracts (pairs of nucleotide combinations) in DNA sequences. Annotated output will include exon/intron regions and tract information.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
TRACTS: A program to map oligopurine.oligopyrimidine and other binary DNA tracts20036
NAR Web Server Issue 2003
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tagsbase composition base sequence dna dna sequence analysis humans p53 genes purines pyrimidines

UniqueProtTool Content

http://cubic.bioc.columbia.edu/services/uniqueprot/ [open in a new window]

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Protein > Sequence Retrieval

UniqueProt creates representative protein sequence sets by eliminating sequence redundancy based on sequence similiarity. This tool needs to be downloaded and run locally on your own machine.

links directory index: 83
TitlePublication YearGoogle Scholar Citation Count
UniqueProt: Creating representative protein sequence sets200383
NAR Web Server Issue 2003
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tagsalgorithms protein sequence analysis proteins sequence alignment tertiary protein structure

VADARTool Content

http://redpoll.pharmacy.ualberta.ca/vadar/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data.

links directory index: 189
TitlePublication YearGoogle Scholar Citation Count
VADAR: a web server for quantitative evaluation of protein structure quality2003189
NAR Web Server Issue 2003
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tagsalgorithms hydrogen bonding molecular structure protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure

Vienna RNA PackageTool Content

http://www.tbi.univie.ac.at/~ivo/RNA/ [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

Comprises a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

links directory index: 945
TitlePublication YearGoogle Scholar Citation Count
Vienna RNA secondary structure server2003945
NAR Web Server Issue 2003
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tagsalgorithms nucleic acid conformation rna rna sequence analysis sequence alignment

WEB-THERMODYNTool Content

http://www.gsa.buffalo.edu/dna/dk/WEBTHERMODYN/ [open in a new window]

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DNA > Structure and Sequence Feature Detection

WEB-THERMODYN analyzes DNA sequences and computes the DNA helical stability. This tool can be used to predict sites of low helical stability present at regulatory regions for transcription and replication.

links directory index: 136
TitlePublication YearGoogle Scholar Citation Count
WEB-THERMODYN: Sequence analysis software for profiling DNA helical stability200332
Ease of DNA unwinding is a conserved property of yeast replication origins1993104
NAR Web Server Issue 2003
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tagsdeoxyribonucleases dna dna replication dna sequence analysis fungal chromosomes fungal dna mutation nucleic acid conformation nucleic acid denaturation nucleic acid regulatory sequences plasmids replication origin replicon saccharomyces cerevisiae thermodynamics

WebFEATURETool Content

http://feature.stanford.edu/webfeature/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.

links directory index: 121
TitlePublication YearGoogle Scholar Citation Count
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures200364
Recognizing protein binding sites using statistical descriptions of their 3D environments199857
NAR Web Server Issue 2003
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tagsalgorithms bayes theorem binding sites calcium calcium-binding proteins computational biology factual databases genomics likelihood functions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein conformation proteins reproducibility of results sensitivity and specificity statistical models

XML Central of DDBJTool Content

http://www.xml.nig.ac.jp/index.html [open in a new window]

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Computer Related > Web Services
Education > Directories and Portals

XML Central of the DNA Data Bank of Japan (DDBJ) provides SOAP (Simple Object Access Protocol) server and web services for various databases and bioinformatics programs.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
Web API for biology with a workflow navigation system200912
Biological SOAP servers and web services provided by the public sequence data bank200329
NAR Web Server Issue 2003
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tagsbiology nucleic acid databases systems integration

XplorMedTool Content

http://www.ogic.ca/projects/xplormed/ [open in a new window]

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Literature > Search Tools
Literature > Text Mining and Semantics

XplorMed is a tool that summarizes MEDLINE search results according to subjects and allows you to navigate through abstracts in an interactive fashion.

links directory index: 134
TitlePublication YearGoogle Scholar Citation Count
Update on XplorMed: A web server for exploring scientific literature200349
Exploring MEDLINE abstracts with XplorMed200214
Computing fuzzy associations for the analysis of biological literature200212
XplorMed: a tool for exploring MEDLINE abstracts200159
NAR Web Server Issue 2003
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YMF 3.0Tool Content

http://wingless.cs.washington.edu/YMF/YMFWeb/YMFInput.pl [open in a new window]

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DNA > Structure and Sequence Feature Detection

YMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs. Multiple organisms are supported including human, yeast, worm, plants, and microbes.

links directory index: 181
TitlePublication YearGoogle Scholar Citation Count
YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation2003181
NAR Web Server Issue 2003
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tagsalgorithms binding sites dna sequence analysis genetic promoter regions mycobacterium tuberculosis nucleic acid regulatory sequences saccharomyces cerevisiae statistical data interpretation transcription factors

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