> Tag > Links tagged with 'molecular sequence data'

Links tagged with 'molecular sequence data'

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Found 156 links

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PREP SuiteTool Content

http://prep.unl.edu/ [open in a new window]

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Model Organisms > Plants
RNA > Motifs

The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial genes, chloroplast genes, and alignments input by the user are included.

This content is being maintained by jpmower.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments200911
PREP-Mt: predictive RNA editor for plant mitochondrial genes200538
NAR Web Server Issue 2009
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tagsamino acid sequence amino acid sequence homology base sequence binding sites chloroplast rna chloroplasts computational biology conserved sequence cytidine dna dna sequence analysis mitochondrial genes mitochondrial proteins molecular sequence data phylogeny plant dna plant gene expression regulation plant genes plant genome plant proteins protein binding protein databases reproducibility of results rna rna editing rna sequence analysis sensitivity and specificity sequence alignment statistical models

PrimacladeTool Content

http://www.umsl.edu/services/kellogg/primaclade.html [open in a new window]

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DNA > Tools For the Bench
Sequence Comparison > Analysis of Aligned Sequences

Primaclade accepts a multiple species nucleotide alignment file as input, iteratively runs the Primer3 application for each sequence, and then collates the results to identify a set of polymerase chain reaction (PCR) primers that will bind across the alignment.

links directory index: 57
TitlePublication YearGoogle Scholar Citation Count
Primaclade--a flexible tool to find conserved PCR primers across multiple species200557
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tagsalgorithms base sequence conserved sequence dna primers dna sequence analysis molecular sequence data nucleic acid sequence homology polymerase chain reaction sequence alignment species specificity

Primer3Tool Content

http://primer3.sourceforge.net/ [open in a new window]

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DNA > Tools For the Bench

Comprehensive PCR primer and hybridization probe design tool; many options but easy to accept defaults at first.

links directory index: 8684
TitlePublication YearGoogle Scholar Citation Count
Primer3 on the WWW for general users and for biologist programmers20008684
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tagsbase sequence database management systems dna primers molecular sequence data nucleic acid sequence homology polymerase chain reaction

PrimerBankDatabase Content

http://pga.mgh.harvard.edu/primerbank/ [open in a new window]

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DNA > Databases
Human Genome > Databases
Model Organisms > Databases

PrimerBank is a public resource for the retrieval of human and mouse primer pairs for gene expression analysis by PCR and Quantitative PCR (QPCR). Information on these primers such as T(m), location on the transcript and amplicon size is also included. For each gene, at least one primer pair has been designed and in many cases alternative primer pairs exist. Primers have been designed to work under the same PCR conditions, thus facilitating high-throughput QPCR. There are several ways to search for primers for the gene(s) of interest, such as by: GenBank accession number, NCBI protein accession number, NCBI gene ID, PrimerBank ID, NCBI gene symbol or gene description (keyword). Primer pairs covering most known mouse genes have been experimentally validated by QPCR, agarose gel analysis, sequencing and BLAST, and all validation data can be freely accessed from the PrimerBank web site.

links directory index: 56
TitlePublication YearGoogle Scholar Citation Count
PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification201056
NAR Database Issue 2010
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tagsanimals base sequence computational biology dna primers gene expression profiling genetic databases humans mice molecular sequence data nucleic acid databases polymerase chain reaction protein databases

PROMALS and PROMALS3DTool Content

http://prodata.swmed.edu/promals3d [open in a new window]

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Sequence Comparison > Multiple Sequence Alignments

PROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.

This content is being maintained by jiminpei.

links directory index: 162
TitlePublication YearGoogle Scholar Citation Count
PROMALS3D web server for accurate multiple protein sequence and structure alignments200823
PROMALS: towards accurate multiple sequence alignments of distantly related proteins2007123
PROMALS web server for accurate multiple protein sequence alignments200716
NAR Web Server Issue 2007NAR Web Server Issue 2008
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tagsalgorithms amino acid sequence amino acid sequence homology computational biology conserved sequence molecular sequence data protein sequence analysis protein structural homology proteins reproducibility of results sensitivity and specificity sequence alignment

PROSITEDatabase Content

http://prosite.expasy.org/ [open in a new window]

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Protein > Databases

PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. PROSITE is used for the annotation of domain features of UniProtKB/Swiss-Prot entries. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases their discriminatory power by providing additional information about functionally and/or structurally critical amino acids.

This content is being maintained by PROSITE.

links directory index: 459
TitlePublication YearGoogle Scholar Citation Count
PROSITE, a protein domain database for functional characterization and annotation2010149
The 20 years of PROSITE.2008310
NAR Database Issue 2010
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tags20th century history 21st century history algorithms amino acid sequence amino acid sequence homology amino acids animals bacterial proteins cluster analysis computational biology genetic databases humans information storage and retrieval internet molecular sequence data nucleic acid databases protein databases protein sequence analysis proteins sequence alignment software tertiary protein structure user-computer interface

Protein Peeling 3 DTool Content

http://www.dsimb.inserm.fr/dsimb_tools/peeling3/ [open in a new window]

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

Protein Peeling is an approach for splitting a protein three dimensional (3D) structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
Protein Peeling 3D: new tools for analyzing protein structures20111
Protein Peeling 2: a web server to convert protein structures into series of protein units200610
'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments200615
NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence chemical models computer simulation molecular models molecular sequence data peptide fragments peptide mapping protein conformation protein folding protein sequence analysis protein subunits proteins statistical models tertiary protein structure

ProtTestTool Content

http://darwin.uvigo.es/software/prottest_server.html [open in a new window]

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Protein > Phylogeny Reconstruction

ProtTest is a program that determines the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment.

links directory index: 1077
TitlePublication YearGoogle Scholar Citation Count
ProtTest: selection of best-fit models of protein evolution20051077
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tagsalgorithms amino acid sequence amino acid substitution amino acids computer simulation dna mutational analysis genetic models humans molecular evolution molecular models molecular sequence data phylogeny protein sequence analysis proteins site-directed mutagenesis structure-activity relationship

PSATool Content

http://bmerc-www.bu.edu/psa/request.htm [open in a new window]

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Protein > 2-D Structure Prediction

Prediction of probable secondary structures and fold-class; good for visualizing amphipathic helices, where present.

links directory index: 324
TitlePublication YearGoogle Scholar Citation Count
Protein classification by stochastic modeling and optimal filtering of amino-acid sequences1994135
Structural analysis based on state-space modeling1993189
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tagsamino acid sequence chemical models flavodoxin markov chains mathematics molecular sequence data molecular structure probability proteins secondary protein structure structural models tertiary protein structure thioredoxins

Pseudomonas Genome DatabaseDatabase Content

http://www.pseudomonas.com [open in a new window]

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Model Organisms > Databases

The Pseudomonas Genome Database integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions, experimental data, and manually curated, community-based annotation updates. Comparative genomics analyses incorporate robust genera-geared methods for predicting and clustering orthologs.

This content is being maintained by fionabrinkman.

links directory index: 2493
TitlePublication YearGoogle Scholar Citation Count
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes20115
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes2009114
Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation200592
Sequencing solution: use volunteer annotators organized via Internet200015
Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen20002267
NAR Database Issue 2011
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external linksLink on Twitter
tagsbacterial dna bacterial gene expression regulation bacterial genes bacterial genome bacterial proteins computational biology dna sequence analysis genetic databases genetic polymorphism genomic islands genomics human genome humans microbial drug resistance molecular sequence data pseudomonas pseudomonas aeruginosa pseudomonas infections species specificity systems integration voluntary workers

Pseudomonas Genome ProjectDatabase Content

http://pseudomonas.com/ [open in a new window]

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Model Organisms > Microbes

This is a comprehensive database on all Pseudomonas species genomes providing primarily access to Pseudomonas aeruginosa genomic data and annotation. Its interface faciliates comparative analyses of genes, proteins, annotations and gene orders, and contains a wealth of additional data including pathway-based, operon-based, protein-localization based, gene function category and ortholog/paralog-based information.

links directory index: 2364
TitlePublication YearGoogle Scholar Citation Count
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes20115
Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation200592
Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen20002267
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external linksLink on Twitter
tagsbacterial dna bacterial gene expression regulation bacterial genome bacterial proteins computational biology dna sequence analysis genetic databases genetic polymorphism genomic islands genomics humans microbial drug resistance molecular sequence data pseudomonas pseudomonas aeruginosa pseudomonas infections software species specificity systems integration user-computer interface

PSEUDOVIEWERTool Content

http://pseudoviewer.inha.ac.kr/ [open in a new window]

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RNA > Structure Prediction, Visualization, and Design

PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures.

This content is being maintained by khan.

links directory index: 139
TitlePublication YearGoogle Scholar Citation Count
PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots200918
PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures200639
PSEUDOVIEWER2: Visualization of RNA pseudoknots of any type200358
PseudoViewer: automatic visualization of RNA pseudoknots200224
NAR Web Server Issue 2003NAR Web Server Issue 2006
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tagsalgorithms base pairing base sequence computational biology molecular models molecular sequence data nucleic acid conformation programming languages rna rna sequence analysis

PSORT.orgTool Content

http://www.psort.org/ [open in a new window]

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Protein > Localization and Targeting

PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.

links directory index: 3330
TitlePublication YearGoogle Scholar Citation Count
PSORTdb: a protein subcellular localization database for bacteria2005101
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria2003292
Extensive feature detection of N-terminal protein sorting signals2002414
PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization19991544
Better prediction of protein cellular localization sites with the k nearest neighbors classifier1997395
Expert system for predicting protein localization sites in gram-negative bacteria1991584
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence bacterial outer membrane proteins bacterial proteins bayes theorem binding sites cell membrane computational biology cytoplasm decision trees escherichia coli evaluation studies as topic expert systems factual databases fungal proteins gram-negative bacteria humans lipoproteins membrane proteins molecular sequence data neural networks (computer) protein databases protein precursors protein sequence analysis protein sorting signals proteins reproducibility of results saccharomyces cerevisiae secondary protein structure sequence alignment subcellular fractions

PSORTdbDatabase Content

http://db.psort.org/ [open in a new window]

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Model Organisms > Microbes
Protein > Localization and Targeting

PSORTdb is a database of proteins of experimentally known (ePSORTdb) and computationally predicted (cPSORTdb) subcellular localization.

links directory index: 101
TitlePublication YearGoogle Scholar Citation Count
PSORTdb: a protein subcellular localization database for bacteria2005101
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tagsbacterial proteins computational biology molecular sequence data protein databases protein sequence analysis

PSORTdbDatabase Content

http://db.psort.org [open in a new window]

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Protein > Databases

PSORTdb (part of the PSORT family) is a database of protein subcellular localizations for bacteria and archaea that contains both information determined through laboratory experimentation (ePSORTdb dataset) and computational predictions (cPSORTdb dataset).

This content is being maintained by fionabrinkman.

links directory index: 107
TitlePublication YearGoogle Scholar Citation Count
PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea20116
PSORTdb: a protein subcellular localization database for bacteria2005101
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsarchaeal proteins bacterial proteins computational biology intracellular space membrane proteins molecular sequence data protein databases protein sequence analysis proteome

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