Volume 31 Issue 13 | Nucleic Acids Research

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Editorial

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Detection of reliable and unexpected protein fold predictions using 3D-Jury

Krzysztof Ginalski; Leszek Rychlewski

Tags: basic local alignment search tool, genome, protein structure

DSSPcont: continuous secondary structure assignments for proteins

Phil Carter; Claus A. F. Andersen; Burkhard Rost

Tags: protein structure, secondary, hydrogen bonding, diagnostic radiologic examination, roentgen rays, protein structure

PROTINFO: secondary and tertiary protein structure prediction

Ling-Hong Hung; Ram Samudrala

Tags: amino acid sequence, protein structure, secondary, tertiary protein structure, wheelchair ramps

The PredictProtein server

Burkhard Rost; Jinfeng Liu

Tags: amino acid sequence, disulfides, electronic mail, internet, nuclear localization signals

GeneSilico protein structure prediction meta-server

Michal A. Kurowski; Janusz M. Bujnicki

Tags: consensus, protein structure, sequence alignment, confidentiality, amino acid sequence

META-PP: single interface to crucial prediction servers

Volker A. Eyrich; Burkhard Rost

Tags: battery, bioinformatics, community, internet, protein structure

EVA: evaluation of protein structure prediction servers

Ingrid Y. Y. Koh; Volker A. Eyrich; Marc A. Marti-Renom; Dariusz Przybylski; Mallur S. Madhusudhan ...

Tags: protein structure, protein structure, secondary, protein data bank

VADAR: a web server for quantitative evaluation of protein structure quality

Leigh Willard; Anuj Ranjan; Haiyan Zhang; Hassan Monzavi; Robert F. Boyko ...

Tags: hydrogen bonding, protein structure, protein structure, secondary, graphical displays, free energy

ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins

Patrice Gouet; Xavier Robert; Emmanuel Courcelle

Tags: basic local alignment search tool, protein data bank, protein structure, secondary, sequence alignment, tertiary protein structure

WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures

Mike P. Liang; D. Rey Banatao; Teri E. Klein; Douglas L. Brutlag; Russ B. Altman

Tags: chimera organism, genomics, models, statistical, molecular structure, nucleic acids

3matrix and 3motif: a protein structure visualization system for conserved sequence motifs

Steven P. Bennett; Lin Lu; Douglas L. Brutlag

Tags: amino acids, color, conserved sequence, internet, protein structure

Motif3D: relating protein sequence motifs to 3D structure

Anna Gaulton; Teresa K. Attwood

Tags: amino acid sequence, cattle, fingerprints, g-protein-coupled receptors, internet

LOC3D: annotate sub-cellular localization for protein structures

Rajesh Nair; Burkhard Rost

Tags: genomics, nuclear localization signals, nuclear proteins, protein data bank, sequence homology

Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures

Alexander Stark; Robert B. Russell

Tags: genomics, databases, protein, benchmarking

NCI: a server to identify non-canonical interactions in protein structures

M. Madan Babu

Tags: national cancer institute, color, peptides, script

MolSurfer: a macromolecular interface navigator

Razif R. Gabdoulline; Rebecca C. Wade; Dirk Walther

Tags: complex, dna, electrostatics, hydrophobicity, macromolecule

CASTp: Computed Atlas of Surface Topography of proteins

T. Andrew Binkowski; Shapor Naghibzadeh; Jie Liang

Tags: casts, surgical, internet, solvents, user-computer interface

SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules

A. S. Z. Hussain; Ch. Kiran Kumar; C. K. Rajesh; S. S. Sheik; K. Sekar

Tags: internet, macromolecule, molecule, crystallography, x-ray, script

Servers for sequence–structure relationship analysis and prediction

Zsuzsanna Dosztányi; Csaba Magyar; Gábor E. Tusnády; Miklós Cserző; András Fiser ...

Tags: cysteine, genome, integral membrane proteins, stabilization, amino acid sequence

POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level

Luigi Cavallo; Jens Kleinjung; Franca Fraternali

Tags: atom, solvents, amino acids, nucleotides, datasets

MATRAS: a program for protein 3D structure comparison

Takeshi Kawabata

Tags: amino acids, libraries

LGA: a method for finding 3D similarities in protein structures

Adam Zemla

Tags: macrosomia

Tools for comparative protein structure modeling and analysis

Narayanan Eswar; Bino John; Nebojsa Mirkovic; Andras Fiser; Valentin A. Ilyin ...

Tags: protein structure, basic local alignment search tool, chest pain units, amino acid substitution

SWISS-MODEL: an automated protein homology-modeling server

Torsten Schwede; Jürgen Kopp; Nicolas Guex; Manuel C. Peitsch

Tags: amino acid sequence, internet, templates, software

STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence

Goran Neshich; Roberto C. Togawa; Adauto L. Mancini; Paula R. Kuser; Michel E. B. Yamagishi ...

Tags: amino acids, instantaneous wave-free ratio, internet, protein structure, sequence alignment

Integrated databanks access and sequence/structure analysis services at the PBIL

Guy Perrière; Christophe Combet; Simon Penel; Christophe Blanchet; Jean Thioulouse ...

Tags: amino acid sequence, base sequence, genbank, genes, internet

NRSAS: Nuclear Receptor Structure Analysis Servers

Emmanuel Bettler; Roland Krause; Florence Horn; Gert Vriend

Tags: receptors, nuclear, nuclear hormone receptor, information systems, mutation, host (organism)

SSEP: secondary structural elements of proteins

V. Shanthi; P. Selvarani; Ch. Kiran Kumar; C. S. Mohire; K. Sekar

Tags: somatosensory evoked potentials, search engine, helix (snails), bioinformatics, physics

Mfold web server for nucleic acid folding and hybridization prediction

Michael Zuker

Tags: dna, nucleic acids, protein structure, secondary, rna, software

RNAsoft: a suite of RNA secondary structure prediction and design software tools

Mirela Andronescu; Rosalía Aguirre-Hernández; Anne Condon; Holger H. Hoos

Tags: protein structure, secondary, rna, software, dna, molecule

Pfold: RNA secondary structure prediction using stochastic context-free grammars

Bjarne Knudsen; Jotun Hein

Tags: protein structure, secondary, rna, models, statistical

Vienna RNA secondary structure server

Ivo L. Hofacker

Tags: protein structure, secondary, rna, software, consensus

PseudoViewer2: visualization of RNA pseudoknots of any type

Kyungsook Han; Yanga Byun

Tags: rna, graphical displays, internet, krypton

A software tool-box for analysis of regulatory RNA elements

Peter Bengert; Thomas Dandekar

Tags: rna, transfer rna, software, trans-splicing

GPRM: a genetic programming approach to finding common RNA secondary structure elements

Yuh-Jyh Hu

Tags: genetics, protein structure, secondary, rna, computers, molecule

Tools for the automatic identification and classification of RNA base pairs

Huanwang Yang; Fabrice Jossinet; Neocles Leontis; Li Chen; John Westbrook ...

Tags: base pairing, rna

GEPAS: a web-based resource for microarray gene expression data analysis

Javier Herrero; Fátima Al-Shahrour; Ramón Díaz-Uriarte; Álvaro Mateos; Juan M. Vaquerizas ...

Tags: gene expression, genes, internet, interval data, gene expression profiling

INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis

Bert Coessens; Gert Thijs; Stein Aerts; Kathleen Marchal; Frank De Smet ...

Tags: clients, computers, gene cluster, gene expression, genes

GenePublisher: automated analysis of DNA microarray data

Steen Knudsen; Christopher Workman; Thomas Sicheritz-Ponten; Carsten Friis

Tags: dna microarrays, signal transduction pathways, genes

ExpressYourself: a modular platform for processing and visualizing microarray data

Nicholas M. Luscombe; Thomas E. Royce; Paul Bertone; Nathaniel Echols; Christine E. Horak ...

Tags: artifacts, binding sites, datasets, dna, dna microarrays

ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis

Sheng Zhong; Cheng Li; Wing Hung Wong

Tags: genes, software, gene annotation

REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data

Crispin Roven; Harmen J. Bussemaker

Tags: dna, genes, genome, oligonucleotides, regulatory sequences, nucleic acid

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays

Henrik Bjørn Nielsen; Rasmus Wernersson; Steen Knudsen

Tags: oligonucleotides

Multiple sequence alignment with the Clustal series of programs

Ramu Chenna; Hideaki Sugawara; Tadashi Koike; Rodrigo Lopez; Toby J. Gibson ...

Tags: bioinformatics, computers, molecular biology, nexus rules, nucleic acids

CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics

Davinder K. Kohli; Anand K. Bachhawat

Tags: internet, nucleic acids, sequence alignment, single nucleotide polymorphism, nucleotides

Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments

Olivier Poirot; Eamonn O'Toole; Cedric Notredame

Tags: coffee, sequence alignment, trees (plant)

SLAM web server for comparative gene finding and alignment

Simon Cawley; Lior Pachter; Marina Alexandersson

Tags: genes, genome, mice, rats, mathematics

Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence

Yvonne J. K. Edwards; Tim J. Carver; Tanya Vavouri; Martin Frith; Martin J. Bishop ...

Tags: binding sites, dna, genome, software, transcription factor

MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences

Scott Schwartz; Laura Elnitski; Mei Li; Matt Weirauch; Cathy Riemer ...

Tags: dna, equus caballus, genome, regulatory sequences, nucleic acid, cattle

MAVID multiple alignment server

Nicolas Bray; Lior Pachter

Tags: genome, mathematics, papio, primates, takifugu

EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae

Liliana Florea; Michael McClelland; Cathy Riemer; Scott Schwartz; Webb Miller

Tags: genome, enterobacteriaceae, genes, preschool imitation and praxis scale, prognosis in palliative care study

MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences

Bernett T. K. Lee; Tin Wee Tan; Shoba Ranganathan

Tags: exons, genome, introns, rna, messenger, rna splicing

RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

Rasmus Wernersson; Anders Gorm Pedersen

Tags: amino acid sequence, dna, amino acids, codon nucleotides, silent mutations

PromH: promoters identification using orthologous genomic sequences

V. V. Solovyev; I. A. Shahmuradov

Tags: genes, genome, oncogenes, tata box, regulatory sequences, nucleic acid

FIE2: a program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes

Allen Chong; Guanglan Zhang; Vladimir B. Bajic

Tags: genes, genome, rna, messenger, dna

PromoSer: a large-scale mammalian promoter and transcription start site identification service

Anason S. Halees; Dmitriy Leyfer; Zhiping Weng

Tags: genes, genome, mammals, mice, oncogenes

Dragon Gene Start Finder identifies approximate locations of the 5′ ends of genes

Vladimir B. Bajic; Seng Hong Seah

Tags: dragon score, genes, cpg islands, oncogenes, exons

ETOPE: evolutionary test of predicted exons

Anton Nekrutenko; Wen-Yu Chung; Wen-Hsiung Li

Tags: exons, expressed sequence tags, genome, computer simulation

ESEfinder: a web resource to identify exonic splicing enhancers

Luca Cartegni; Jinhua Wang; Zhengwei Zhu; Michael Q. Zhang; Adrian R. Krainer

Tags: consensus, enhancer of transcription, exons, mutation, point mutation

SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences

Paul E. Boardman; Stephen G. Oliver; Simon J. Hubbard

Tags: base sequence, binding sites, genes, transcription factor, dna

MATCH^TM: a tool for searching transcription factor binding sites in DNA sequences

A.E. Kel; E. Gößling; I. Reuter; E. Cheremushkin; O.V. Kel-Margoulis ...

Tags: binding sites, dna, transcription factor, libraries, gene expression regulation

Gibbs Recursive Sampler: finding transcription factor binding sites

William Thompson; Eric C. Rouchka; Charles E. Lawrence

Tags: binding sites, dna, heterogeneity, internet, transcription factor

YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation

Saurabh Sinha; Martin Tompa

Tags: binding sites, genes, transcription factor, software, dna

Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors

Alona Sosinsky; Christopher P. Bonin; Richard S. Mann; Barry Honig

Tags: binding sites, candidate disease gene, genome, libraries, transcription factor

Regulatory Sequence Analysis Tools

Jacques van Helden

Tags: dna, genome, sequence analysis, streptococcal antigen test, rapid, genbank

GeneSeqer@PlantGDB: gene structure prediction in plant genomes

Shannon D. Schlueter; Qunfeng Dong; Volker Brendel

Tags: expressed sequence tags, gene organization, genes, genome, genome, plant

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders

William H. Majoros; Mihaela Pertea; Corina Antonescu; Steven L. Salzberg

Tags: arabidopsis, decision trees, eukaryotic cell, genes, myoc gene

Dragon ERE Finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes

Vladimir B. Bajic; Sin Lam Tan; Allen Chong; Suisheng Tang; Anders Ström ...

Tags: dna, dragon score, estrogen, genes, genome

PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences

Giorgio Grillo; Flavio Licciulli; Sabino Liuni; Elisabetta Sbisà; Graziano Pesole

Tags: base sequence, consensus sequence, dna, gene expression regulation, genome

PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria

Jennifer L. Gardy; Cory Spencer; Ke Wang; Martin Ester; Gábor E. Tusnády ...

Tags: amino acids, datasets, gram-negative bacteria, mental recall, peptides

Signal search analysis server

Giovanna Ambrosini; Viviane Praz; Vidhya Jagannathan; Philipp Bucher

Tags: calr gene, consensus, software

MHCPred: a server for quantitative prediction of peptide–MHC binding

Pingping Guan; Irini A. Doytchinova; Christianna Zygouri; Darren R. Flower

Tags: hla-a antigens, hla-a2 antigen, peptides, alleles, epitopes, t-lymphocyte

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins

Pål Puntervoll; Rune Linding; Christine Gemünd; Sophie Chabanis-Davidson; Morten Mattingsdal ...

Tags: embryonic lethal mutation, filters

Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Π, NMT and PTS1

Frank Eisenhaber; Birgit Eisenhaber; Werner Kubina; Sebastian Maurer-Stroh; Georg Neuberger ...

Tags: amino acids, eukaryotic cell, fungus, lipids, plants

Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs

John C. Obenauer; Lewis C. Cantley; Michael B. Yaffe

Tags: amino acid sequence, databases, protein, electrophoresis, gel, two-dimensional, isoelectric point, molecular mass

Static benchmarking of membrane helix predictions

Andrew Kernytsky; Burkhard Rost

Tags: benchmarking, helix (snails), tissue membrane, hydrophobicity, signal sequences, peptide

The web server of IBM's Bioinformatics and Pattern Discovery group

Tien Huynh; Isidore Rigoutsos; Laxmi Parida; Daniel Platt; Tetsuo Shibuya

Tags: base sequence, bioinformatics, genes, sequence alignment, amino acid sequence

Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN

Domènec Farré; Romà Roset; Mario Huerta; José E. Adsuara; Llorenç Roselló ...

Tags: binding sites, dna, internet, transcription factor, genome

SEARCHPKS: a program for detection and analysis of polyketide synthase domains

Gitanjali Yadav; Rajesh S. Gokhale; Debasisa Mohanty

Tags: acyltransferase, biosynthesis, genome, guidelines, natural products

MAK, a computational tool kit for automated MITE analysis

Guojun Yang; Timothy C. Hall

Tags: mites, transposase, mathematics, genes, dna transposable elements

Cluster-Buster: finding dense clusters of motifs in DNA sequences

Martin C. Frith; Michael C. Li; Zhiping Weng

Tags: dna, genome, transcription factor, enhancer of transcription, regulatory sequences, nucleic acid

SIC: a tool to detect short inverted segments in a biological sequence

David Robelin; Hugues Richard; Bernard Prum

Tags: dna, software

mreps
: efficient and flexible detection of tandem repeats in DNA

Roman Kolpakov; Ghizlane Bana; Gregory Kucherov

Tags: dna, genome, tandem repeat sequences, software

SPA: simple web tool to assess statistical significance of DNA patterns

H. Richard; G. Nuel

Tags: dna, mathematics, genome, expert systems

TRACTS: a program to map oligopurine.oligopyrimidine and other binary DNA tracts

Moshe Gal; Tzvi Katz; Amir Ovadia; Gad Yagil

Tags: dna, genes, genome, introns, exons

DNA analysis servers: plot.it, bend.it, model.it and IS

Kristian Vlahoviček; László Kaján; Sándor Pongor

Tags: base composition, dna, dna analysis, exons, introns

NEBcutter: a program to cleave DNA with restriction enzymes

Tamas Vincze; Janos Posfai; Richard J. Roberts

Tags: dna, dna restriction enzymes, enzymes, digestion, dna methylation

SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence

C.Z. Cai; L.Y. Han; Z.L. Ji; X. Chen; Y.Z. Chen

Tags: internet, software, sequence alignment, seeds

BPROMPT: a consensus server for membrane protein prediction

Paul D. Taylor; Teresa K. Attwood; Darren R. Flower

Tags: anatomy, regional, consensus, membrane proteins, internet, eukaryotic cell

GlobPlot: exploring protein sequences for globularity and disorder

Rune Linding; Robert B. Russell; Victor Neduva; Toby J. Gibson

Tags: benchmarking, genomics, peptides, protein structure, proteome

iSPOT: a web tool to infer the interaction specificity of families of protein modules

Barbara Brannetti; Manuela Helmer-Citterich

Tags: complex, ligands, peptides, tertiary protein structure, amino acid sequence

Automated Gene Ontology annotation for anonymous sequence data

Steffen Hennig; Detlef Groth; Hans Lehrach

Tags: genes, genome, databases, protein, vocabulary, dna, complementary

ESTAnnotator: a tool for high throughput EST annotation

Agnes Hotz-Wagenblatt; Thomas Hankeln; Peter Ernst; Karl-Heinz Glatting; Erwin R. Schmidt ...

Tags: basic local alignment search tool, bioinformatics, cartilage, dna, expressed sequence tags

Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes

François Enault; Karsten Suhre; Olivier Poirot; Chantal Abergel; Jean-Michel Claverie

Tags: genes, genes, bacterial, genome, genome, bacterial, neighborhood

AMIGene: Annotation of MIcrobial Genes

Stéphanie Bocs; Stéphane Cruveiller; David Vallenet; Grégory Nuel; Claudine Médigue

Tags: decision support systems, clinical, genes, genome, genome, bacterial, heuristics

AHMII: Agent to Help Microbial Information Integration

Hideaki Sugawara; Satoru Miyazaki

Tags: bacteria, cell line, fungus, microorganisms, molecular biology

DNannotator: annotation software tool kit for regional genomic sequences

Chunyu Liu; Tom I. Bonner; Tu Nguyen; Jennifer L. Lyons; Susan L. Christian ...

Tags: genome, single nucleotide polymorphism, software, genes, genbank

Bioverse: functional, structural and contextual annotation of proteins and proteomes

Jason McDermott; Ram Samudrala

Tags: proteome, genome, genomics, internet

FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences

Thomas Schiex; Jérôme Gouzy; Annick Moisan; Yannick de Oliveira

Tags: frameshift mutation function, genes, genome

EUGÈNE'HOM: a generic similarity-based gene finder using multiple homologous sequences

Sylvain Foissac; Philippe Bardou; Annick Moisan; Marie-Josée Cros; Thomas Schiex

Tags: genes, software, plants, models, statistical, codon, initiator

PROBEmer: a web-based software tool for selecting optimal DNA oligos

Scott J. Emrich; Mary Lowe; Arthur L. Delcher

Tags: dna, genes, internet, oligonucleotides, polymerase chain reaction

Primer Design Assistant (PDA): a web-based primer design tool

S.H. Chen; C.Y. Lin; C.S. Cho; C.Z. Lo; C.A. Hsiung

Tags: apache, chest pain units, dimers, internet, polymerase chain reaction

DePIE: Designing Primers for Protein Interaction Experiments

Guoqing Lu; Michael Hallett; Stephanie Pollock; David Thomas

Tags: base sequence, body temperature, clone cells, internet, peptides

OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling

Niels Tolstrup; Peter S. Nielsen; Jens G. Kolberg; Annett M. Frankel; Henrik Vissing ...

Tags: gene expression profiling, nucleic acids, oligonucleotides, genes, basic local alignment search tool

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design

Timothy M. Rose; Jorja G. Henikoff; Steven Henikoff

Tags: amino acids, codon nucleotides, consensus, oligonucleotides, polymerase chain reaction

RNA-related tools on the Bielefeld Bioinformatics Server

Alexander Sczyrba; Jan Krüger; Henning Mersch; Stefan Kurtz; Robert Giegerich

Tags: bioinformatics, rna, protein structure, secondary

SIRW: a web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches

Chenna Ramu

Tags: bioinformatics, community, internet, sequence analysis

Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate

Sorin Draghici; Purvesh Khatri; Pratik Bhavsar; Abhik Shah; Stephen A. Krawetz ...

Tags: genes, opportunity for error, chromosomes, vortex formation

Swiss EMBnet node web server

Laurent Falquet; Lorenza Bordoli; Vassilios Ioannidis; Marco Pagni; C. Victor Jongeneel

Tags: bioinformatics, sequence analysis, software

ExPASy: the proteomics server for in-depth protein knowledge and analysis

Elisabeth Gasteiger; Alexandre Gattiker; Christine Hoogland; Ivan Ivanyi; Ron D. Appel ...

Tags: proteomics, biological sciences, bioinformatics, enzymes, protein processing, post-translational

UniqueProt: creating representative protein sequence sets

Sven Mika; Burkhard Rost

Tags: amino acid sequence, datasets

BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases

Konstantinos Bimpikis; Aidan Budd; Rune Linding; Toby J. Gibson

Tags: basic local alignment search tool, datasets, search engine

WU-Blast2 server at the European Bioinformatics Institute

Rodrigo Lopez; Ville Silventoinen; Stephen Robinson; Asif Kibria; Warren Gish

Tags: basic local alignment search tool, bioinformatics, software, internet

OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms

Günther Zehetner

Tags: basic local alignment search tool, genes, genome

ORFeus: detection of distant homology using sequence profiles and predicted secondary structure

Krzysztof Ginalski; Jakub Pas; Lucjan S. Wyrwicz; Marcin von Grotthuss; Janusz M. Bujnicki ...

Tags: protein structure, secondary, community, amino acid sequence

PARSESNP: a tool for the analysis of nucleotide polymorphisms

Nicholas E. Taylor; Elizabeth A. Greene

Tags: genes, nucleotides, polymorphism, dna, dna restriction enzymes

SIFT: predicting amino acid changes that affect protein function

Pauline C. Ng; Steven Henikoff

Tags: amino acid substitution, amino acids, single nucleotide polymorphism, mutagenesis, polymorphism

ActionMap: a web-based software that automates loci assignments to framework maps

Guillaume Albini; Matthieu Falque; Johann Joets

Tags: internet, maps, software, plants, script

WEB-THERMODYN: sequence analysis software for profiling DNA helical stability

Yanlin Huang; David Kowalski

Tags: dna, software, free energy, sequence analysis, regulatory sequences, nucleic acid

NEWT, a new taxonomy portal

I. Q. H. Phan; S. F. Pilbout; W. Fleischmann; A. Bairoch

Tags: newts, taxonomic classification

Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription

Michal Lapidot; Yitzhak Pilpel

Tags: rna, messenger, community, computational biology, diagnosis

PipeAlign: a new toolkit for protein family analysis

Frédéric Plewniak; Laurent Bianchetti; Yann Brelivet; Annaick Carles; Frédéric Chalmel ...

Tags: sequence alignment, software

NORSp: predictions of long regions without regular secondary structure

Jinfeng Liu; Burkhard Rost

Tags: protein structure, secondary, amino acid sequence

Biological SOAP servers and web services provided by the public sequence data bank

H. Sugawara; S. Miyazaki

Tags: heterogeneity, internet, software, xml

FootPrinter: a program designed for phylogenetic footprinting

Mathieu Blanchette; Martin Tompa

Tags: regulatory sequences, nucleic acid, software

GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives

Edouard Yeramian; Louis Jones

Tags: dna, genes, genetics, genome, helix (snails)

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes

Niko Beerenwinkel; Martin Däumer; Mark Oette; Klaus Korn; Daniel Hoffmann ...

Tags: drug resistance, genotype, phenotype, r factors, hiv-1

Building protein diagrams on the web with the residue-based diagram editor RbDe

Lucy Skrabanek; Fabien Campagne; Harel Weinstein

Tags: anatomy, regional, gene organization, g-protein-coupled receptors, integral membrane proteins, internet

CRP: Cleavage of Radiolabeled Phosphoproteins

Aaron J. Mackey; Timothy A.J. Haystead; William R. Pearson

Tags: cytokinesis, phosphoproteins, phosphorylation, radioactivity, proteolysis

JVirGel: calculation of virtual two-dimensional protein gels

Karsten Hiller; Max Schobert; Claudia Hundertmark; Dieter Jahn; Richard Münch

Tags: gel, isoelectric point, proteome, hydrophobicity, proteomics

Update on XplorMed: a web server for exploring scientific literature

Carolina Perez-Iratxeta; Antonio J. Pérez; Peer Bork; Miguel A. Andrade

Tags: medline

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