> Tag > Links tagged with 'protein sequence analysis'

Links tagged with 'protein sequence analysis'

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Found 226 links

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TreeSAAPTool Content

http://dna.cs.byu.edu/treesaap/ [open in a new window]

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Sequence Comparison > Analysis of Aligned Sequences

The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during clade-genesis, and performs goodness-of-fit and categorical statistical tests.

links directory index: 78
TitlePublication YearGoogle Scholar Citation Count
TreeSAAP: selection on amino acid properties using phylogenetic trees200378
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tagsamino acid sequence genetic variation molecular evolution molecular sequence data phylogeny protein sequence analysis proteins

trimAlTool Content

http://trimal.cgenomics.org [open in a new window]

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Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments

trimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.

This content is being maintained by tgabaldon.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses200964
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tagsalgorithms computational biology editing multiple sequence alignment multiple sequence alignment phylogeny protein sequence analysis sequence alignment trimming multiple sequence alignment

TSEMATool Content

http://tsema.bioinfo.cnio.es/ [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

The Server for Efficient Mapping Assessment (TSEMA) predicts possible protein-protein interactions based on the comparision of phylogenetic trees derived from sequences of associated protein families.

links directory index: 325
TitlePublication YearGoogle Scholar Citation Count
TSEMA: interactive prediction of protein pairings between interacting families200616
Similarity of phylogenetic trees as indicator of protein-protein interaction2001309
NAR Web Server Issue 2006
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tagsbacterial genome chaperonin 60 computational biology escherichia coli proteins glutamate-trna ligase gtp-binding proteins molecular evolution monte carlo method phylogeny protein interaction mapping protein sequence analysis proteins proteome ribosomal proteins sequence alignment statistics as topic tertiary protein structure

UniPROBEDatabase Content

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

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Protein > Databases

The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions201114
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsanimals binding sites dna dna-binding proteins humans protein array analysis protein databases protein sequence analysis

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

Universal Protein Resource (UniProt)Database Content

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

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Protein > Databases

Universal Protein Resource (UniProt) maintains a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database.

links directory index: 1408
TitlePublication YearGoogle Scholar Citation Count
Reorganizing the protein space at the Universal Protein Resource (UniProt)201213
Ongoing and future developments at the Universal Protein Resource2011154
The Universal Protein Resource (UniProt) in 2010201053
The Universal Protein Resource (UniProt)20071170
Update on genome completion and annotations: Protein Information Resource200418
NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms amino acid sequence animals computational biology europe fungal genome human genome humans nucleic acid databases protein databases protein isoforms protein sequence analysis proteins proteome proteomics systems integration viral genome

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

VKCDBDatabase Content

http://vkcdb.biology.ualberta.ca [open in a new window]

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DNA > Databases
Protein > Databases

The Voltage-gated K(+) Channel DataBase (VKCDB) contains full-length or nearly full-length unique channel sequences from Bacteria, Archaea and Eukaryotes. Corresponding nucleotide sequences of the open reading frames corresponding to the amino acid sequences are now available and can be extracted in parallel with sets of protein sequences. Channels are categorized into subfamilies by phylogenetic analysis and by using hidden Markov model analyses. The retrieval function of the web interface allows retrieval of entries that contain a substantial fraction of the core structural elements of VKCs, fragmentary entries, or both. The full database can be downloaded as either a MySQL dump or as an XML dump from the web site.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
VKCDB: voltage-gated K+ channel database updated and upgraded20111
NAR Database Issue 2011
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tagsarchaeal proteins bacterial proteins open reading frames phylogeny protein databases protein sequence analysis voltage-gated potassium channels

VOMBATTool Content

https://www2.informatik.uni-halle.de:8443/VOMBAT/faces/pages/choose.jsp [open in a new window]

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DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

VOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees.

links directory index: 99
TitlePublication YearGoogle Scholar Citation Count
VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees20069
Identification of transcription factor binding sites with variable-order Bayesian networks200590
NAR Web Server Issue 2006
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tagsalgorithms artificial intelligence bayes theorem binding sites chemical models computer simulation genomics markov chains molecular models protein binding protein databases protein sequence analysis sequence alignment statistical models structure-activity relationship transcription factors transcriptional regulatory elements

WAViSTool Content

http://wavis.img.cas.cz/ [open in a new window]

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DNA > DNA and Genomic Analysis
Protein > Identification, Presentation and Format
Sequence Comparison > Alignment Editing and Visualization

The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
WAViS server for handling, visualization and presentation of multiple alignments of nucleotide or amino acids sequences20044
NAR Web Server Issue 2004
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tagsdna sequence analysis humans protein sequence analysis rna sequence analysis sequence alignment sequence analysis

WDACTool Content

http://pat.kobic.re.kr/wdac/index.htm [open in a new window]

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Protein > Domains and Motifs
Protein > Sequence Comparison

The WDAC (Weighted Domain Architecture Comparison Tool) is a web-based server to perform protein homology search by comparing protein domain architectures, defined as a sequential order of domains in a protein.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
Protein comparison at the domain architecture level20098
DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture20088
NAR Web Server Issue 2008
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tagscomputational biology protein databases protein sequence analysis protein structural homology proteins tertiary protein structure

WebScipio - eukaryotic gene identificationTool Content

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

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DNA > Gene Prediction
Expression > Splicing
RNA > General Resources
Sequence Comparison > Analysis of Aligned Sequences

Scipio is a tool to determine the precise exon-intron gene structure given a protein sequence and a genome. It identifies splice sites and is able to cope with sequencing errors and genes spanning several contigs. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in related species. WebScipio, allows to search for mutually exclusive spliced exons and tandemly arrayed gene duplicates.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
WebScipio: an online tool for the determination of gene structures using protein sequences20089
Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species200815
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tagsacetylcholine action potentials algorithms alternative splicing amino acid sequence animals apomorphine atropine base sequence benserazide bromocriptine central nervous system dextroamphetamine diaphragm dna sequence analysis dopamine drosophila melanogaster drosophila proteins epinephrine exon-intron structure exons extrapyramidal tracts female gene duplicates gene prediction gene structure genetic databases genomics haloperidol human parainfluenza virus 3 humans hydroxylamines immunologic deficiency syndromes infant introns kinetics levodopa mathematics molecular sequence data motor activity muscle contraction muscle denervation mutually exclusive splicing nerve degeneration neurological models neuromuscular junction nucleic acid sequence homology oxidation-reduction paramyxoviridae infections physostigmine piribedil planarians protein sequence analysis proteins rats reading frames reserpine rna splice sites sequence alignment software species specificity superoxide dismutase superoxides synaptic transmission tandem gene duplication tetrodotoxin turbellaria user-computer interface viral pneumonia x chromosome

WoLF PSORTTool Content

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

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Protein > Localization and Targeting

WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction.

links directory index: 463
TitlePublication YearGoogle Scholar Citation Count
WoLF PSORT: protein localization predictor2007463
NAR Web Server Issue 2007
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tagsarabidopsis computational biology humans membrane proteins programming languages protein databases protein sequence analysis protein sorting signals proteins reproducibility of results secondary protein structure statistical models

WurstTool Content

http://www.zbh.uni-hamburg.de/wurst/ [open in a new window]

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Protein > 3-D Structure Prediction

Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures.

links directory index: 42
TitlePublication YearGoogle Scholar Citation Count
Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices200442
NAR Web Server Issue 2004
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tagsamino acid substitution molecular models protein conformation protein sequence analysis

xREITool Content

http://biowiki.org/XreiProgram [open in a new window]

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DNA > DNA and Genomic Analysis
DNA > Gene Prediction
Protein > 2-D Structure Prediction
RNA > Functional RNAs

xREI is a web interface that allows users to explore a range of predefined phylo-grammars or create their own phylo-grammar. Grammars are visualized via state transition graphs and substitution matrices. xREI is based on xrate, the flexible software tool for modeling structural and phylogenetic variation in multiple sequence alignments.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
xREI: a phylo-grammar visualization webserver20081
NAR Web Server Issue 2008
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tagsdna sequence analysis phylogeny protein sequence analysis rna sequence analysis sequence alignment statistical models

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